Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images. - Robert F. Murphy; Michael V. Boland; Meel Velliste (ISMB, 2000)

Searching Online Journals for Fluorescence Microscope Images Depicting Protein Subcellular Location Patterns. - Robert F. Murphy; Meel Velliste; Jie Yao; Gregory Porreca (BIBE, 2001)

A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. - Michael V. Boland; Robert F. Murphy (Bioinform., 2001)

Image content-based retrieval and automated interpretation of fluorescence microscope images via the protein subcellular location image database. - Kai Huang; Jennifer Lin; James A. Gajnak; Robert F. Murphy (ISBI, 2002)

Automated determination of protein subcellular locations from 3D fluorescence microscope images. - Meel Velliste; Robert F. Murphy (ISBI, 2002)

Robust classification of subcellular location patterns in fluorescence microscope images. - Robert F. Murphy; Meel Velliste; Gregory Porreca (NNSP, 2002)

Understanding captions in biomedical publications. - William W. Cohen; Richard C. Wang; Robert F. Murphy (KDD, 2003)

Extracting information from text and images for location proteomics. - Zhenzhen Kou; William W. Cohen; Robert F. Murphy (BIOKDD, 2003)

Robust Numerical Features for Description and Classification of Subcellular Location Patterns in Fluorescence Microscope Images. - Robert F. Murphy; Meel Velliste; Gregory Porreca (J. VLSI Signal Process., 2003)

Automated Classification of Subcellular Patterns In Multicell Images Without Segmentation Into Single Cells. - Kai Huang; Robert F. Murphy (ISBI, 2004)

Automated Interpretation of Subcellular Location Patterns. - Robert F. Murphy (ISBI, 2004)

Boosting accuracy of automated classification of fluorescence microscope images for location proteomics. - Kai Huang; Robert F. Murphy (BMC Bioinform., 2004)

A Distributed Database for BioMolecular Images. - Ambuj K. Singh; B. S. Manjunath; Robert F. Murphy (SIGMOD Rec., 2004)

Data Mining Methods for a Systematics of Protein Subcellular Location. - Kai Huang; Robert F. Murphy (Data Mining in Bioinformatics, 2005)

Adaptive Multirate Data Acquisition of 3D Cell Images. - Thomas E. Merryman; Jelena Kovacevic; Elvira Garcia Osuna; Robert F. Murphy (ICASSP (2), 2005)

High-recall protein entity recognition using a dictionary. - Zhenzhen Kou; William W. Cohen; Robert F. Murphy (ISMB (Supplement of Bioinformatics), 2005)

Research issues in protein location image databases. - Robert F. Murphy; Christos Faloutsos (SIGMOD Conference, 2005)

Object Type Recognition for Automated Analysis of Protein Subcellular Location. - Ting Zhao; Meel Velliste; Michael V. Boland; Robert F. Murphy (IEEE Trans. Image Process., 2005)

A Novel Graphical Model Approach to Segmenting Cell Images. - Shann-Ching Chen; Ting Zhao; Geoffrey J. Gordon; Robert F. Murphy (CIBCB, 2006)

A novel approximate inference approach to automated classification of protein subcellular location patterns in multi-cell images. - Shann-Ching Chen; Geoffrey J. Gordon; Robert F. Murphy (ISBI, 2006)

Topology preserving STACS segmentation of protein subcellular location images. - Lionel Coulot; Heather Kirschner; Amina Chebira; José M. F. Moura; Jelena Kovacevic; Elvira Garcia Osuna; Robert F. Murphy (ISBI, 2006)

Application of temporal texture features to automated analysis of protein subcellular locations in time series fluorescence microscope images. - Yanhua Hu; Jesus Carmona; Robert F. Murphy (ISBI, 2006)

Improved comparison of protein subcellular location patterns. - Ting Zhao; Stalia Soto; Robert F. Murphy (ISBI, 2006)

A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images. - Shann-Ching Chen; Robert F. Murphy (BMC Bioinform., 2006)

Molecular and cellular bioimaging [Guest editorial]. - Jelena Kovacevic; Robert F. Murphy (IEEE Signal Process. Mag., 2006)

Interpretation of Protein Subcellular Location Patterns in 3D Images Across Cell Types and Resolutions. - Xiang Chen; Robert F. Murphy (BIRD, 2007)

Efficient Acquisition and Learning of Fluorescence Microscope Data Models. - Charles Jackson; Robert F. Murphy; Jelena Kovacevic (ICIP (6), 2007)

Identifying Fluorescence Microscope Images in Online Journal Articles Using Both Image and Text Features. - Juchang Hua; Orhan N. Ayasli; William W. Cohen; Robert F. Murphy (ISBI, 2007)

Systematic Description of Subcellular Location for Integration with Proteomics Databases and Systems Biology Modeling. - Robert F. Murphy (ISBI, 2007)

Automated image analysis of protein localization in budding yeast. - Shann-Ching Chen; Ting Zhao; Geoffrey J. Gordon; Robert F. Murphy (ISMB/ECCB (Supplement of Bioinformatics), 2007)

A Stacked Graphical Model for Associating Sub-Images with Sub-Captions. - Zhenzhen Kou; William W. Cohen; Robert F. Murphy (Pacific Symposium on Biocomputing, 2007)

A multiresolution approach to automated classification of protein subcellular location images. - Amina Chebira; Yann Barbotin; Charles Jackson; Thomas E. Merryman; Gowri Srinivasa; Robert F. Murphy; Jelena Kovacevic (BMC Bioinform., 2007)

Identifying Subcellular Locations from Images of Unknown Resolution. - Luís Pedro Coelho; Robert F. Murphy (BIRD, 2008)

Automated comparison of protein subcellular location patterns between images of normal and cancerous tissues. - Estelle Glory; Justin Newberg; Robert F. Murphy (ISBI, 2008)

Automated proteome-wide determination of subcellular location using high throughput microscopy. - Robert F. Murphy (ISBI, 2008)

Deformation-based nonlinear dimension reduction: Applications to nuclear morphometry. - Gustavo K. Rohde; Wei Wang 037; Tao Peng 004; Robert F. Murphy (ISBI, 2008)

Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature. - Luís Pedro Coelho; Amr Ahmed 001; Andrew Arnold; Joshua D. Kangas; Abdul-Saboor Sheikh; Eric P. Xing; William W. Cohen; Robert F. Murphy (BioLINK@ISMB/ECCB, 2008)

Principles of Bioimage Informatics: Focus on Machine Learning of Cell Patterns. - Luís Pedro Coelho; Estelle Glory-Afshar; Joshua D. Kangas; Shannon Quinn; Aabid Shariff; Robert F. Murphy (BioLINK@ISMB/ECCB, 2008)

Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. - Yuntao Qian; Robert F. Murphy (Bioinform., 2008)

Graphical Models for Structured Classification, with an Application to Interpreting Images of Protein Subcellular Location Patterns. - Shann-Ching Chen; Geoffrey J. Gordon; Robert F. Murphy (J. Mach. Learn. Res., 2008)

Workshop summary: Automated interpretation and modelling of cell images. - Robert F. Murphy; Chun-Nan Hsu; Loris Nanni (ICML, 2009)

Nuclear Segmentation in Microscope Cell Images: A Hand-Segmented Dataset and Comparison of Algorithms. - Luís Pedro Coelho; Aabid Shariff; Robert F. Murphy (ISBI, 2009)

Automated Analysis of Human Protein Atlas Immunofluorescence Images. - Justin Newberg; Jieyue Li; Arvind Rao; Fredrik Ponten; Mathias Uhlen; Emma Lundberg; Robert F. Murphy (ISBI, 2009)

Instance-Based Generative Biological Shape Modeling. - Tao Peng 004; Wei Wang 037; Gustavo K. Rohde; Robert F. Murphy (ISBI, 2009)

Structured correspondence topic models for mining captioned figures in biological literature. - Amr Ahmed 001; Eric P. Xing; William W. Cohen; Robert F. Murphy (KDD, 2009)

Intelligent Acquisition and Learning of Fluorescence Microscope Data Models. - Charles Jackson; Robert F. Murphy; Jelena Kovacevic (IEEE Trans. Image Process., 2009)

A graphical model to determine the subcellular protein location in artificial tissues. - Estelle Glory-Afshar; Elvira Osuna-Highley; Brian Granger; Robert F. Murphy (ISBI, 2010)

Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing. - Luís Pedro Coelho; Tao Peng 004; Robert F. Murphy (Bioinform., 2010)

Automated analysis of protein subcellular location in time series images. - Yanhua Hu; Elvira Osuna-Highley; Juchang Hua; Theodore Scott Nowicki; Robert Stolz; Camille McKayle; Robert F. Murphy (Bioinform., 2010)

Structured literature image finder: Parsing text and figures in biomedical literature. - Amr Ahmed 001; Andrew Arnold; Luís Pedro Coelho; Joshua D. Kangas; Abdul-Saboor Sheikh; Eric P. Xing; William W. Cohen; Robert F. Murphy (J. Web Semant., 2010)

Determination of protein location diversity via analysis of immunohistochemical images from the Human Protein Atlas. - Arvind Rao; Robert F. Murphy (ISBI, 2011)

Automated estimation of microtubule model parameters from 3-D live cell microscopy images. - Aabid Shariff; Robert F. Murphy; Gustavo K. Rohde (ISBI, 2011)

Model building and intelligent acquisition with application to protein subcellular location classification. - Charles Jackson; Estelle Glory-Afshar; Robert F. Murphy; Jelena Kovacevic (Bioinform., 2011)

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. - Tien-ho Lin; Ziv Bar-Joseph; Robert F. Murphy (J. Comput. Biol., 2011)

Discriminative Motif Finding for Predicting Protein Subcellular Localization. - Tien-ho Lin; Robert F. Murphy; Ziv Bar-Joseph (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

(3) The CellOrganizer project: An open source system to learn image-derived models of subcellular organization over time and space. - Robert F. Murphy (BIBM, 2012)

Protein subcellular location pattern classification in cellular images using latent discriminative models. - Jieyue Li; Liang Xiong; Jeff G. Schneider; Robert F. Murphy (Bioinform., 2012)

Determining the subcellular location of new proteins from microscope images using local features. - 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 (Bioinform., 2013)

Using Analytics for Improving Implementation Fidelity in an Large Scale Efficacy Trial. - Mingyu Feng; Jeremy Roschelle; Robert F. Murphy; Neil T. Heffernan (ICLS, 2014)

Implementation of an Intelligent Tutoring System for Online Homework Support in an Efficacy Trial. - Mingyu Feng; Jeremy Roschelle; Neil T. Heffernan; Janet Fairman; Robert F. Murphy (Intelligent Tutoring Systems, 2014)

A new era in bioimage informatics. - Robert F. Murphy (Bioinform., 2014)

Efficient discovery of responses of proteins to compounds using active learning. - Joshua D. Kangas; Armaghan W. Naik; Robert F. Murphy (BMC Bioinform., 2014)

Design Automation for Biological Models: A Pipeline that Incorporates Spatial and Molecular Complexity. - Devin P. Sullivan; Rohan Arepally; Robert F. Murphy; José Juan Tapia; James R. Faeder; Markus Dittrich; Jacob Czech (ACM Great Lakes Symposium on VLSI, 2015)

Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions (Extended Abstract). - Maja Temerinac-Ott; Armaghan W. Naik; Robert F. Murphy (RECOMB, 2015)

Deciding when to stop: efficient experimentation to learn to predict drug-target interactions. - Maja Temerinac-Ott; Armaghan W. Naik; Robert F. Murphy (BMC Bioinform., 2015)

Deciding when to stop: Efficient stopping of active learning guided drug-target prediction. - Maja Temerinac-Ott; Armaghan W. Naik; Robert F. Murphy (CoRR, 2015)

Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules. - Gregory R. Johnson; Jieyue Li; Aabid Shariff; Gustavo K. Rohde; Robert F. Murphy (PLoS Comput. Biol., 2015)

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. - Rory M. Donovan; José Juan Tapia; Devin P. Sullivan; James R. Faeder; Robert F. Murphy; Markus Dittrich; Daniel M. Zuckerman (PLoS Comput. Biol., 2016)

Image-based spatiotemporal causality inference for protein signaling networks. - Xiongtao Ruan; Christoph Wülfing; Robert F. Murphy (Bioinform., 2017)

Learning Generative Models of Tissue Organization with Supervised GANs. - Ligong Han; Robert F. Murphy; Deva Ramanan (WACV, 2018)

Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes. - Jose Lugo-Martinez; Jörn Dengjel; Ziv Bar-Joseph; Robert F. Murphy (BCB, 2019)

Evaluation of methods for generative modeling of cell and nuclear shape. - Xiongtao Ruan; Robert F. Murphy (Bioinform., 2019)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - 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; et al. (Nat., 2019)

Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization. - Timothy Majarian; Robert F. Murphy; Seema S. Lakdawala (PLoS Comput. Biol., 2019)

Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images. - Ying-Ying Xu; Hong-Bin Shen; Robert F. Murphy (Bioinform., 2020)

Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery. - Huangqingbo Sun; Robert F. Murphy (Bioinform., 2021)

Improving and evaluating deep learning models of cellular organization. - Huangqingbo Sun; Xuecong Fu; Serena Abraham; Shen Jin; Robert F. Murphy (Bioinform., 2022)

Implementing and Evaluating ASSISTments Online Math Homework Support At large Scale over Two Years: Findings and Lessons Learned. - Mingyu Feng; Neil T. Heffernan; Kelly Collins; Cristina Heffernan; Robert F. Murphy (AIED, 2023)

SBML level 3 package: spatial processes, version 1, release 1. - James C. Schaff; Anuradha Lakshminarayana; Robert F. Murphy; Frank T. Bergmann; Akira Funahashi; Devin P. Sullivan; Lucian P. Smith (J. Integr. Bioinform., 2023)

Expanding the coverage of spatial proteomics: a machine learning approach. - Huangqingbo Sun; Jiayi Li; Robert F. Murphy (Bioinform., 2024)