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ORCIDAnne E. Carpenter
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- affiliation: Broad Institute of MIT and Harvard, Cambridge, USA
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Journal Articles
- 2024
[j18]Srijit Seal
, Ola Spjuth, Layla Hosseini-Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender, Anne E. Carpenter:
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. J. Chem. Inf. Model. 64(4): 1172-1186 (2024)- [j17]Robert van Dijk, John Arevalo, Mehrtash Babadi, Anne E. Carpenter, Shantanu Singh:
Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning. PLoS Comput. Biol. 20(11): 1012547 (2024) - 2022
- [j16]Yuen Ler Chow, Shantanu Singh, Anne E. Carpenter, Gregory P. Way:
Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic. PLoS Comput. Biol. 18(2) (2022) - 2021
- [j15]David R. Stirling, Anne E. Carpenter, Beth A. Cimini:
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis. Bioinform. 37(21): 3992-3994 (2021) - [j14]David R. Stirling, Madison J. Swain-Bowden, Alice M. Lucas, Anne E. Carpenter, Beth A. Cimini, Allen Goodman:
CellProfiler 4: improvements in speed, utility and usability. BMC Bioinform. 22(1): 433 (2021) - 2020
- [j13]Jane Hung, Allen Goodman, Deepali Ravel, Stefanie Lopes, Gabriel Rangel, Odailton A. Nery, Benoit Malleret, Francois Nosten, Marcus V. G. Lacerda, Marcelo U. Ferreira, Laurent Rénia, Manoj Duraisingh, Fabio T. M. Costa, Matthias Marti, Anne E. Carpenter:
Keras R-CNN: library for cell detection in biological images using deep neural networks. BMC Bioinform. 21(1): 300 (2020) - [j12]Anne E. Carpenter:
Bridging Domain and Data. Patterns 1(4): 100064 (2020) - 2019
- [j11]Victor Kulikov, Syuan-Ming Guo, Matthew Stone, Allen Goodman, Anne E. Carpenter, Mark Bathe, Victor S. Lempitsky:
DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images. PLoS Comput. Biol. 15(5) (2019) - 2016
- [j10]David Dao, Adam Fraser, Jane Hung, Vebjorn Ljosa, Shantanu Singh, Anne E. Carpenter:
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets. Bioinform. 32(20): 3210-3212 (2016) - [j9]Virginie Uhlmann, Shantanu Singh, Anne E. Carpenter:
CP-CHARM: segmentation-free image classification made accessible. BMC Bioinform. 17: 51 (2016) - [j8]Cleber C. Melo-Filho, Rafael Ferreira Dantas, Rodolpho C. Braga, Bruno Junior Neves, Mario R. Senger, Walter C. G. Valente, João M. Rezende-Neto, Willian T. Chaves, Eugene N. Muratov, Ross A. Paveley, Nicholas Furnham, Lee Kamentsky, Anne E. Carpenter, Floriano Silva-Junior, Carolina Horta Andrade:
QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. J. Chem. Inf. Model. 56(7): 1357-1372 (2016) - 2015
- [j7]Mark-Anthony Bray, Anne E. Carpenter:
CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data. BMC Bioinform. 16: 369:1-369:7 (2015) - 2014
- [j6]Imtiaz A. Khan, Adam Fraser, Mark-Anthony Bray, Paul J. Smith, Nick S. White, Anne E. Carpenter, Rachel J. Errington:
ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments. Bioinform. 30(23): 3440-3442 (2014) - 2011
- [j5]Lee Kamentsky, Thouis R. Jones, Adam Fraser, Mark-Anthony Bray, David J. Logan, Katherine L. Madden, Vebjorn Ljosa, Curtis Rueden, Kevin W. Eliceiri, Anne E. Carpenter:
Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinform. 27(8): 1179-1180 (2011) - [j4]A. Johannes Pretorius, Mark-Anthony Bray, Anne E. Carpenter, Roy A. Ruddle:
Visualization of Parameter Space for Image Analysis. IEEE Trans. Vis. Comput. Graph. 17(12): 2402-2411 (2011) - 2009
- [j3]Björn Nilsson, Mikael Johansson, Fátima Al-Shahrour, Anne E. Carpenter, Benjamin L. Ebert:
Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. Bioinform. 25(8): 1078-1079 (2009) - [j2]Vebjorn Ljosa, Anne E. Carpenter:
Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening. PLoS Comput. Biol. 5(12) (2009) - 2008
- [j1]Thouis R. Jones, In Han Kang, Douglas B. Wheeler, Robert A. Lindquist, Adam Papallo, David M. Sabatini, Polina Golland, Anne E. Carpenter:
CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinform. 9 (2008)
Conference and Workshop Papers
- 2023
- [c12]Marzieh Haghighi, Mario C. Cruz, Erin Weisbart, Beth A. Cimini, Avtar Singh, Julia Bauman, Maria E. Lozada, Sanam L. Kavari, James T. Neal, Paul C. Blainey, Anne E. Carpenter, Shantanu Singh:
Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images. IJCAI 2023: 4775-4784 - 2019
- [c11]Maxime W. Lafarge, Juan C. Caicedo, Anne E. Carpenter, Josien P. W. Pluim, Shantanu Singh, Mitko Veta:
Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning. MIDL 2019: 315-325 - 2018
- [c10]Juan C. Caicedo, Claire McQuin, Allen Goodman, Shantanu Singh, Anne E. Carpenter:
Weakly Supervised Learning of Single-Cell Feature Embeddings. CVPR 2018: 9309-9318 - [c9]Tim Becker, Juan C. Caicedo, Shantanu Singh, Markus Weckmann, Anne E. Carpenter:
Combining morphological and migration profiles of in vitro time-lapse data. ISBI 2018: 965-968 - 2017
- [c8]Jane Hung, Anne E. Carpenter:
Applying Faster R-CNN for Object Detection on Malaria Images. CVPR Workshops 2017: 808-813 - 2015
- [c7]Topaz Gilad, Mark-Anthony Bray, Anne E. Carpenter, Tammy Riklin Raviv:
Symmetry-based mitosis detection in time-lapse microscopy. ISBI 2015: 164-167 - [c6]Assaf Arbelle, N. Drayman, Mark-Anthony Bray, U. Alon, Anne E. Carpenter, Tammy Riklin Raviv:
Analysis of High-throughput Microscopy Videos: Catching Up with Cell Dynamics. MICCAI (3) 2015: 218-225 - 2014
- [c5]Anne E. Carpenter:
Behavior in the Time of Cholera: Evidence from the 2008-2009 Cholera Outbreak in Zimbabwe. SBP 2014: 237-244 - 2011
- [c4]Anne E. Carpenter:
Extracting biomedically important information from large, automated imaging experiments. ISBI 2011: 1723-1726 - 2010
- [c3]Carolina Wählby, Tammy Riklin-Raviv, Vebjorn Ljosa, Annie L. Conery, Polina Golland, Frederick M. Ausubel, Anne E. Carpenter:
Resolving clustered worms via probabilistic shape models. ISBI 2010: 552-555 - [c2]Tammy Riklin Raviv, Vebjorn Ljosa, Annie L. Conery, Frederick M. Ausubel, Anne E. Carpenter, Polina Golland, Carolina Wählby:
Morphology-Guided Graph Search for Untangling Objects: C. elegans Analysis. MICCAI (3) 2010: 634-641 - 2005
- [c1]Thouis R. Jones, Anne E. Carpenter, Polina Golland:
Voronoi-Based Segmentation of Cells on Image Manifolds. CVBIA 2005: 535-543
Informal and Other Publications
- 2024
- [i7]John Arevalo, Ellen Su, Anne E. Carpenter, Shantanu Singh:
MOTIVE: A Drug-Target Interaction Graph For Inductive Link Prediction. CoRR abs/2406.08649 (2024) - [i6]Gang Liu, Srijit Seal, John Arevalo, Zhenwen Liang, Anne E. Carpenter, Meng Jiang, Shantanu Singh:
Learning Molecular Representation in a Cell. CoRR abs/2406.12056 (2024) - 2023
- [i5]Marzieh Haghighi, Mario C. Cruz, Erin Weisbart, Beth A. Cimini, Avtar Singh, Julia Bauman, Maria E. Lozada, Sanam L. Kavari, James T. Neal, Paul C. Blainey, Anne E. Carpenter, Shantanu Singh:
Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images. CoRR abs/2306.15898 (2023) - 2021
- [i4]Anne E. Carpenter, Casey S. Greene, Piero Carnici, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley, Kim-Anh Lê Cao, Jerry S. H. Lee, Luigi Marchionni, Suzanne Sindi, Fabian J. Theis, Gregory P. Way, Jean Y. H. Yang, Elana J. Fertig:
A field guide to cultivating computational biology. CoRR abs/2104.11364 (2021) - [i3]Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase:
Developing open-source software for bioimage analysis: opportunities and challenges. F1000Research 10: 302 (2021) - 2018
- [i2]Jane Hung, Allen Goodman, Stefanie Lopes, Gabriel Rangel, Deepali Ravel, Fabio T. M. Costa, Manoj Duraisingh, Matthias Marti, Anne E. Carpenter:
Applying Faster R-CNN for Object Detection on Malaria Images. CoRR abs/1804.09548 (2018) - 2010
- [i1]Mayank Kabra, Annie L. Conery, Eyleen J. O'Rourke, Xin Xie, Vebjorn Ljosa, Thouis R. Jones, Frederick M. Ausubel, Gary Ruvkun, Anne E. Carpenter, Yoav Freund:
Towards automated high-throughput screening of C. elegans on agar. CoRR abs/1003.4287 (2010)
Coauthor Index
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