Robert F. Murphy

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 19

Top Topics

Boltzmann Machine

Protein Complexes

Active Learning

Top Venues

PLoS Comput. Biol.

Publications

Huangqingbo Sun, Jiayi Li, Robert F. Murphy
Expanding the coverage of spatial proteomics: a machine learning approach. Bioinform. 40 (2) (2024)
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)
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)
Huangqingbo Sun, Xuecong Fu, Serena Abraham, Shen Jin, Robert F. Murphy
Improving and evaluating deep learning models of cellular organization. Bioinform. 38 (23) (2022)
Huangqingbo Sun, Robert F. Murphy
Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery. Bioinform. 37 (20) (2021)
Ying-Ying Xu, Hong-Bin Shen, Robert F. Murphy
Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images. Bioinform. 36 (6) (2020)
Ligong Han, Robert F. Murphy, Deva Ramanan
Learning Generative Models of Tissue Organization with Supervised GANs. CoRR (2020)
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)
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)
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 deCaestecker, 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 A. 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) (2019)
Xiongtao Ruan, Robert F. Murphy
Evaluation of methods for generative modeling of cell and nuclear shape. Bioinform. 35 (14) (2019)
Ligong Han, Robert F. Murphy, Deva Ramanan
Learning Generative Models of Tissue Organization with Supervised GANs. WACV (2018)
Xiongtao Ruan, Christoph Wülfing, Robert F. Murphy
Image-based spatiotemporal causality inference for protein signaling networks. Bioinform. 33 (14) (2017)
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)
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)
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 (2015)
Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy
Deciding when to stop: Efficient stopping of active learning guided drug-target prediction. CoRR (2015)
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)
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)
Joshua D. Kangas, Armaghan W. Naik, Robert F. Murphy
Efficient discovery of responses of proteins to compounds using active learning. BMC Bioinform. 15 (2014)
Robert F. Murphy
A new era in bioimage informatics. Bioinform. 30 (10) (2014)
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) (2013)
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)
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) (2012)
Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. RECOMB (2011)
Aabid Shariff, Robert F. Murphy, Gustavo K. Rohde
Automated estimation of microtubule model parameters from 3-D live cell microscopy images. ISBI (2011)
Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. J. Comput. Biol. 18 (11) (2011)
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) (2011)
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) (2011)
Arvind Rao, Robert F. Murphy
Determination of protein location diversity via analysis of immunohistochemical images from the Human Protein Atlas. ISBI (2011)
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) (2010)
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)
Luís Pedro Coelho, Tao Peng, Robert F. Murphy
Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing. Bioinform. 26 (12) (2010)
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) (2010)
Tao Peng, Wei Wang, Gustavo K. Rohde, Robert F. Murphy
Instance-Based Generative Biological Shape Modeling. ISBI (2009)
Charles Jackson, Robert F. Murphy, Jelena Kovacevic
Intelligent Acquisition and Learning of Fluorescence Microscope Data Models. IEEE Trans. Image Process. 18 (9) (2009)
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)
Amr Ahmed, Eric P. Xing, William W. Cohen, Robert F. Murphy
Structured correspondence topic models for mining captioned figures in biological literature. KDD (2009)
Luís Pedro Coelho, Aabid Shariff, Robert F. Murphy
Nuclear Segmentation in Microscope Cell Images: A Hand-Segmented Dataset and Comparison of Algorithms. ISBI (2009)
Robert F. Murphy, Chun-Nan Hsu, Loris Nanni
Workshop summary: Automated interpretation and modelling of cell images. ICML (2009)
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)
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 (2008)
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)
Yuntao Qian, Robert F. Murphy
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. Bioinform. 24 (4) (2008)
Robert F. Murphy
Automated proteome-wide determination of subcellular location using high throughput microscopy. ISBI (2008)
Estelle Glory, Justin Newberg, Robert F. Murphy
Automated comparison of protein subcellular location patterns between images of normal and cancerous tissues. ISBI (2008)
Luís Pedro Coelho, Robert F. Murphy
Identifying Subcellular Locations from Images of Unknown Resolution. BIRD (2008)
Gustavo K. Rohde, Wei Wang, Tao Peng, Robert F. Murphy
Deformation-based nonlinear dimension reduction: Applications to nuclear morphometry. ISBI (2008)
Xiang Chen, Robert F. Murphy
Interpretation of Protein Subcellular Location Patterns in 3D Images Across Cell Types and Resolutions. BIRD (2007)
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)
Robert F. Murphy
Systematic Description of Subcellular Location for Integration with Proteomics Databases and Systems Biology Modeling. ISBI (2007)
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)
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)
Zhenzhen Kou, William W. Cohen, Robert F. Murphy
A Stacked Graphical Model for Associating Sub-Images with Sub-Captions. Pacific Symposium on Biocomputing (2007)
Charles Jackson, Robert F. Murphy, Jelena Kovacevic
Efficient Acquisition and Learning of Fluorescence Microscope Data Models. ICIP (6) (2007)
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)
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)
Ting Zhao, Stalia Soto, Robert F. Murphy
Improved comparison of protein subcellular location patterns. ISBI (2006)
Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, Robert F. Murphy
A Novel Graphical Model Approach to Segmenting Cell Images. CIBCB (2006)
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 (2006)
Jelena Kovacevic, Robert F. Murphy
Molecular and cellular bioimaging [Guest editorial]. IEEE Signal Process. Mag. 23 (3) (2006)
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)
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) (2005)
Thomas E. Merryman, Jelena Kovacevic, Elvira Garcia Osuna, Robert F. Murphy
Adaptive Multirate Data Acquisition of 3D Cell Images. ICASSP (2) (2005)
Zhenzhen Kou, William W. Cohen, Robert F. Murphy
High-recall protein entity recognition using a dictionary. ISMB (Supplement of Bioinformatics) (2005)
Robert F. Murphy, Christos Faloutsos
Research issues in protein location image databases. SIGMOD Conference (2005)
Kai Huang, Robert F. Murphy
Automated Classification of Subcellular Patterns In Multicell Images Without Segmentation Into Single Cells. ISBI (2004)
Kai Huang, Robert F. Murphy
Boosting accuracy of automated classification of fluorescence microscope images for location proteomics. BMC Bioinform. 5 (2004)
Ambuj K. Singh, B. S. Manjunath, Robert F. Murphy
A Distributed Database for BioMolecular Images. SIGMOD Rec. 33 (2) (2004)
Robert F. Murphy
Automated Interpretation of Subcellular Location Patterns. ISBI (2004)
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) (2003)
William W. Cohen, Richard C. Wang, Robert F. Murphy
Understanding captions in biomedical publications. KDD (2003)
Zhenzhen Kou, William W. Cohen, Robert F. Murphy
Extracting information from text and images for location proteomics. BIOKDD (2003)
Meel Velliste, Robert F. Murphy
Automated determination of protein subcellular locations from 3D fluorescence microscope images. ISBI (2002)
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)
Robert F. Murphy, Meel Velliste, Gregory Porreca
Robust classification of subcellular location patterns in fluorescence microscope images. NNSP (2002)
Robert F. Murphy, Meel Velliste, Jie Yao, Gregory Porreca
Searching Online Journals for Fluorescence Microscope Images Depicting Protein Subcellular Location Patterns. BIBE (2001)
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) (2001)
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)