Robert F. Murphy

84 papers A* 3A 3B 3C 2Misc 1Journal 36Unranked 34
YearRankTypeTitle / Venue / Authors
2025 J jnl
CytoSpatio: Learning cell type spatial relationships using multirange, multitype point process models.
PLoS Comput. Biol.
Haoran Chen, Yangyuan Zhang, Robert F. Murphy
2024 J jnl
Expanding the coverage of spatial proteomics: a machine learning approach.
Bioinform.
Huangqingbo Sun, Jiayi Li, Robert F. Murphy
2023 A conf
Implementing and Evaluating ASSISTments Online Math Homework Support At large Scale over Two Years: Findings and Lessons Learned.
AIED
Mingyu Feng, Neil T. Heffernan, Kelly Collins, Cristina Heffernan, Robert F. Murphy
2023 J jnl
SBML level 3 package: spatial processes, version 1, release 1.
J. Integr. Bioinform.
James C. Schaff, Anuradha Lakshminarayana, Robert F. Murphy, Frank T. Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian P. Smith
2022 J jnl
Improving and evaluating deep learning models of cellular organization.
Bioinform.
Huangqingbo Sun, Xuecong Fu, Serena Abraham, Shen Jin, Robert F. Murphy
2021 J jnl
Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery.
Bioinform.
Huangqingbo Sun, Robert F. Murphy
2020 J jnl
Learning Generative Models of Tissue Organization with Supervised GANs.
CoRR
Ligong Han, Robert F. Murphy, Deva Ramanan
2020 J jnl
Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images.
Bioinform.
Ying-Ying Xu, Hong-Bin Shen, Robert F. Murphy
2019 J jnl
Evaluation of methods for generative modeling of cell and nuclear shape.
Bioinform.
Xiongtao Ruan, Robert F. Murphy
2019 — conf
Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes.
BCB
Jose Lugo-Martinez, Jörn Dengjel, Ziv Bar-Joseph, Robert F. Murphy
2019 J jnl
Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization.
PLoS Comput. Biol.
Timothy Majarian, Robert F. Murphy, Seema S. Lakdawala
2019 J jnl
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
Nat.
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
2018 A conf
Learning Generative Models of Tissue Organization with Supervised GANs.
WACV
Ligong Han, Robert F. Murphy, Deva Ramanan
2017 J jnl
Image-based spatiotemporal causality inference for protein signaling networks.
Bioinform.
Xiongtao Ruan, Christoph Wülfing, Robert F. Murphy
2016 J jnl
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories.
PLoS Comput. Biol.
Rory M. Donovan, José Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman
2015 J jnl
Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules.
PLoS Comput. Biol.
Gregory R. Johnson, Jieyue Li, Aabid Shariff, Gustavo K. Rohde, Robert F. Murphy
2015 B conf
Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions (Extended Abstract).
RECOMB
Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy
2015 J jnl
Deciding when to stop: Efficient stopping of active learning guided drug-target prediction.
CoRR
Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy
2015 J jnl
Deciding when to stop: efficient experimentation to learn to predict drug-target interactions.
BMC Bioinform.
Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy
2015 — conf
Design Automation for Biological Models: A Pipeline that Incorporates Spatial and Molecular Complexity.
ACM Great Lakes Symposium on VLSI
Devin P. Sullivan, Rohan Arepally, Robert F. Murphy, José Juan Tapia, James R. Faeder, Markus Dittrich, Jacob Czech
2014 J jnl
A new era in bioimage informatics.
Bioinform.
Robert F. Murphy
2014 J jnl
Efficient discovery of responses of proteins to compounds using active learning.
BMC Bioinform.
Joshua D. Kangas, Armaghan W. Naik, Robert F. Murphy
2014 B conf
Implementation of an Intelligent Tutoring System for Online Homework Support in an Efficacy Trial.
Intelligent Tutoring Systems
Mingyu Feng, Jeremy Roschelle, Neil T. Heffernan, Janet Fairman, Robert F. Murphy
2014 — conf
Using Analytics for Improving Implementation Fidelity in an Large Scale Efficacy Trial.
ICLS
Mingyu Feng, Jeremy Roschelle, Robert F. Murphy, Neil T. Heffernan
2013 J jnl
Determining the subcellular location of new proteins from microscope images using local features.
Bioinform.
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
2012 — conf
(3) The CellOrganizer project: An open source system to learn image-derived models of subcellular organization over time and space.
BIBM
Robert F. Murphy
2012 J jnl
Protein subcellular location pattern classification in cellular images using latent discriminative models.
Bioinform.
Jieyue Li, Liang Xiong, Jeff G. Schneider, Robert F. Murphy
2011 — conf
Automated estimation of microtubule model parameters from 3-D live cell microscopy images.
ISBI
Aabid Shariff, Robert F. Murphy, Gustavo K. Rohde
2011 — conf
Determination of protein location diversity via analysis of immunohistochemical images from the Human Protein Atlas.
ISBI
Arvind Rao, Robert F. Murphy
2011 J jnl
Discriminative Motif Finding for Predicting Protein Subcellular Localization.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tien-ho Lin, Robert F. Murphy, Ziv Bar-Joseph
2011 B conf
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs.
RECOMB
Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy
2011 J jnl
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs.
J. Comput. Biol.
Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy
2011 J jnl
Model building and intelligent acquisition with application to protein subcellular location classification.
Bioinform.
Charles Jackson, Estelle Glory-Afshar, Robert F. Murphy, Jelena Kovacevic
2010 — conf
A graphical model to determine the subcellular protein location in artificial tissues.
ISBI
Estelle Glory-Afshar, Elvira Osuna-Highley, Brian Granger, Robert F. Murphy
2010 J jnl
Automated analysis of protein subcellular location in time series images.
Bioinform.
Yanhua Hu, Elvira Osuna-Highley, Juchang Hua, Theodore Scott Nowicki, Robert Stolz, Camille McKayle, Robert F. Murphy
2010 J jnl
Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing.
Bioinform.
Luís Pedro Coelho, Tao Peng, Robert F. Murphy
2010 J jnl
Structured literature image finder: Parsing text and figures in biomedical literature.
J. Web Semant.
Amr Ahmed, Andrew Arnold, Luís Pedro Coelho, Joshua D. Kangas, Abdul-Saboor Sheikh, Eric P. Xing, William W. Cohen, Robert F. Murphy
2009 — conf
Automated Analysis of Human Protein Atlas Immunofluorescence Images.
ISBI
Justin Newberg, Jieyue Li, Arvind Rao, Fredrik Ponten, Mathias Uhlen, Emma Lundberg, Robert F. Murphy
2009 — conf
Instance-Based Generative Biological Shape Modeling.
ISBI
Tao Peng, Wei Wang, Gustavo K. Rohde, Robert F. Murphy
2009 J jnl
Intelligent Acquisition and Learning of Fluorescence Microscope Data Models.
IEEE Trans. Image Process.
Charles Jackson, Robert F. Murphy, Jelena Kovacevic
2009 — conf
Nuclear Segmentation in Microscope Cell Images: A Hand-Segmented Dataset and Comparison of Algorithms.
ISBI
Luís Pedro Coelho, Aabid Shariff, Robert F. Murphy
2009 A* conf
Structured correspondence topic models for mining captioned figures in biological literature.
KDD
Amr Ahmed, Eric P. Xing, William W. Cohen, Robert F. Murphy
2009 A* conf
Workshop summary: Automated interpretation and modelling of cell images.
ICML
Robert F. Murphy, Chun-Nan Hsu, Loris Nanni
2008 — conf
Automated comparison of protein subcellular location patterns between images of normal and cancerous tissues.
ISBI
Estelle Glory, Justin Newberg, Robert F. Murphy
2008 — conf
Automated proteome-wide determination of subcellular location using high throughput microscopy.
ISBI
Robert F. Murphy
2008 — ed.
Bioinformatics Research and Development, Second International Conference, BIRD 2008, Vienna, Austria, July 7-9, 2008, Proceedings
BIRD
Mourad Elloumi, Josef Küng, Michal Linial, Robert F. Murphy, Kristan Schneider, Cristian Toma
2008 — conf
Deformation-based nonlinear dimension reduction: Applications to nuclear morphometry.
ISBI
Gustavo K. Rohde, Wei Wang, Tao Peng, Robert F. Murphy
2008 J jnl
Graphical Models for Structured Classification, with an Application to Interpreting Images of Protein Subcellular Location Patterns.
J. Mach. Learn. Res.
Shann-Ching Chen, Geoffrey J. Gordon, Robert F. Murphy
2008 — conf
Identifying Subcellular Locations from Images of Unknown Resolution.
BIRD
Luís Pedro Coelho, Robert F. Murphy
2008 J jnl
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models.
Bioinform.
Yuntao Qian, Robert F. Murphy
2008 — conf
Principles of Bioimage Informatics: Focus on Machine Learning of Cell Patterns.
BioLINK@ISMB/ECCB
Luís Pedro Coelho, Estelle Glory-Afshar, Joshua D. Kangas, Shannon Quinn, Aabid Shariff, Robert F. Murphy
2008 — conf
Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature.
BioLINK@ISMB/ECCB
Luís Pedro Coelho, Amr Ahmed, Andrew Arnold, Joshua D. Kangas, Abdul-Saboor Sheikh, Eric P. Xing, William W. Cohen, Robert F. Murphy
2007 Misc conf
A Stacked Graphical Model for Associating Sub-Images with Sub-Captions.
Pacific Symposium on Biocomputing
Zhenzhen Kou, William W. Cohen, Robert F. Murphy
2007 J jnl
A multiresolution approach to automated classification of protein subcellular location images.
BMC Bioinform.
Amina Chebira, Yann Barbotin, Charles Jackson, Thomas E. Merryman, Gowri Srinivasa, Robert F. Murphy, Jelena Kovacevic
2007 — conf
Automated image analysis of protein localization in budding yeast.
ISMB/ECCB (Supplement of Bioinformatics)
Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, Robert F. Murphy
2007 — conf
Efficient Acquisition and Learning of Fluorescence Microscope Data Models.
ICIP (6)
Charles Jackson, Robert F. Murphy, Jelena Kovacevic
2007 — conf
Identifying Fluorescence Microscope Images in Online Journal Articles Using Both Image and Text Features.
ISBI
Juchang Hua, Orhan N. Ayasli, William W. Cohen, Robert F. Murphy
2007 — conf
Interpretation of Protein Subcellular Location Patterns in 3D Images Across Cell Types and Resolutions.
BIRD
Xiang Chen, Robert F. Murphy
2007 — conf
Systematic Description of Subcellular Location for Integration with Proteomics Databases and Systems Biology Modeling.
ISBI
Robert F. Murphy
2006 C conf
A Novel Graphical Model Approach to Segmenting Cell Images.
CIBCB
Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, Robert F. Murphy
2006 J jnl
A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images.
BMC Bioinform.
Shann-Ching Chen, Robert F. Murphy
2006 — conf
A novel approximate inference approach to automated classification of protein subcellular location patterns in multi-cell images.
ISBI
Shann-Ching Chen, Geoffrey J. Gordon, Robert F. Murphy
2006 — conf
Application of temporal texture features to automated analysis of protein subcellular locations in time series fluorescence microscope images.
ISBI
Yanhua Hu, Jesus Carmona, Robert F. Murphy
2006 — conf
Improved comparison of protein subcellular location patterns.
ISBI
Ting Zhao, Stalia Soto, Robert F. Murphy
2006 J jnl
Molecular and cellular bioimaging [Guest editorial].
IEEE Signal Process. Mag.
Jelena Kovacevic, Robert F. Murphy
2006 — conf
Topology preserving STACS segmentation of protein subcellular location images.
ISBI
Lionel Coulot, Heather Kirschner, Amina Chebira, José M. F. Moura, Jelena Kovacevic, Elvira Garcia Osuna, Robert F. Murphy
2005 — conf
Adaptive Multirate Data Acquisition of 3D Cell Images.
ICASSP (2)
Thomas E. Merryman, Jelena Kovacevic, Elvira Garcia Osuna, Robert F. Murphy
2005 — ch.
Data Mining Methods for a Systematics of Protein Subcellular Location.
Data Mining in Bioinformatics
Kai Huang, Robert F. Murphy
2005 — conf
High-recall protein entity recognition using a dictionary.
ISMB (Supplement of Bioinformatics)
Zhenzhen Kou, William W. Cohen, Robert F. Murphy
2005 J jnl
Object Type Recognition for Automated Analysis of Protein Subcellular Location.
IEEE Trans. Image Process.
Ting Zhao, Meel Velliste, Michael V. Boland, Robert F. Murphy
2005 — conf
Research issues in protein location image databases.
SIGMOD Conference
Robert F. Murphy, Christos Faloutsos
2004 J jnl
A Distributed Database for BioMolecular Images.
SIGMOD Rec.
Ambuj K. Singh, B. S. Manjunath, Robert F. Murphy
2004 — conf
Automated Classification of Subcellular Patterns In Multicell Images Without Segmentation Into Single Cells.
ISBI
Kai Huang, Robert F. Murphy
2004 — conf
Automated Interpretation of Subcellular Location Patterns.
ISBI
Robert F. Murphy
2004 J jnl
Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.
BMC Bioinform.
Kai Huang, Robert F. Murphy
2003 — conf
Extracting information from text and images for location proteomics.
BIOKDD
Zhenzhen Kou, William W. Cohen, Robert F. Murphy
2003 J jnl
Robust Numerical Features for Description and Classification of Subcellular Location Patterns in Fluorescence Microscope Images.
J. VLSI Signal Process.
Robert F. Murphy, Meel Velliste, Gregory Porreca
2003 A* conf
Understanding captions in biomedical publications.
KDD
William W. Cohen, Richard C. Wang, Robert F. Murphy
2002 — conf
Automated determination of protein subcellular locations from 3D fluorescence microscope images.
ISBI
Meel Velliste, Robert F. Murphy
2002 — conf
Image content-based retrieval and automated interpretation of fluorescence microscope images via the protein subcellular location image database.
ISBI
Kai Huang, Jennifer Lin, James A. Gajnak, Robert F. Murphy
2002 — conf
Robust classification of subcellular location patterns in fluorescence microscope images.
NNSP
Robert F. Murphy, Meel Velliste, Gregory Porreca
2001 J jnl
A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells.
Bioinform.
Michael V. Boland, Robert F. Murphy
2001 C conf
Searching Online Journals for Fluorescence Microscope Images Depicting Protein Subcellular Location Patterns.
BIBE
Robert F. Murphy, Meel Velliste, Jie Yao, Gregory Porreca
2000 A conf
Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images.
ISMB
Robert F. Murphy, Michael V. Boland, Meel Velliste