Learning Molecular Representation in a Cell

Authors: Liu, Gang, Seal, Srijit, Arevalo, John, Liang, Zhenwen, Carpenter, Anne E., Jiang, Meng, Singh, Shantanu

Subject Terms: Computer Science - Machine Learning, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2406.12056

MOTIVE: A Drug-Target Interaction Graph For Inductive Link Prediction

Authors: Arevalo, John, Su, Ellen, Carpenter, Anne E, Singh, Shantanu

Subject Terms: Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2406.08649

A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

Authors: Seal, Srijit, Trapotsi, Maria-Anna, Spjuth, Ola, Singh, Shantanu, Carreras-Puigvert, Jordi, Greene, Nigel, Bender, Andreas, Carpenter, Anne E.

Subject Terms: Quantitative Biology - Subcellular Processes, Quantitative Biology - Cell Behavior

Access URL: http://arxiv.org/abs/2405.02767

Cell Painting Gallery: an open resource for image-based profiling

Authors: Weisbart, Erin, Kumar, Ankur, Arevalo, John, Carpenter, Anne E., Cimini, Beth A., Singh, Shantanu

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2402.02203

Reproducible image-based profiling with Pycytominer

Authors: Serrano, Erik, Chandrasekaran, Srinivas Niranj, Bunten, Dave, Brewer, Kenneth I., Tomkinson, Jenna, Kern, Roshan, Bornholdt, Michael, Fleming, Stephen, Pei, Ruifan, Arevalo, John, Tsang, Hillary, Rubinetti, Vincent, Tromans-Coia, Callum, Becker, Tim, Weisbart, Erin, Bunne, Charlotte, Kalinin, Alexandr A., Senft, Rebecca, Taylor, Stephen J., Jamali, Nasim, Adeboye, Adeniyi, Abbasi, Hamdah Shafqat, Goodman, Allen, Caicedo, Juan C., Carpenter, Anne E., Cimini, Beth A., Singh, Shantanu, Way, Gregory P.

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2311.13417

Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images

Authors: Haghighi, Marzieh, Cruz, Mario C., Weisbart, Erin, Cimini, Beth A., Singh, Avtar, Bauman, Julia, Lozada, Maria E., Kavari, Sanam L., Neal, James T., Blainey, Paul C., Carpenter, Anne E., Singh, Shantanu

Source: Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence (IJCAI), Main Track, Pages 4775-4784, 2023

Subject Terms: Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2306.15898

Pervasive mislocalization of pathogenic coding variants underlying human disorders

Authors: Lacoste, Jessica, Haghighi, Marzieh, Haider, Shahan, Reno, Chloe, Lin, Zhen-Yuan, Segal, Dmitri, Qian, Wesley Wei, Xiong, Xueting, Teelucksingh, Tanisha, Miglietta, Esteban, Shafqat-Abbasi, Hamdah, Ryder, Pearl V., Senft, Rebecca, Cimini, Beth A., Murray, Ryan R., Nyirakanani, Chantal, Hao, Tong, McClain, Gregory G., Roth, Frederick P., Calderwood, Michael A., Hill, David E., Vidal, Marc, Yi, S. Stephen, Sahni, Nidhi, Peng, Jian, Gingras, Anne-Claude, Singh, Shantanu, Carpenter, Anne E., Taipale, Mikko

Source: In Cell 14 November 2024 187(23):6725-6741

CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis

Authors: Stirling, David R., Carpenter, Anne E., Cimini, Beth A.

Source: Bioinformatics, 2021; btab634

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2108.02060

A field guide to cultivating computational biology

Authors: Carpenter, Anne E, Greene, Casey S, Carnici, Piero, Carvalho, Benilton S, de Hoon, Michiel, Finley, Stacey, Cao, Kim-Anh Le, Lee, Jerry SH, Marchionni, Luigi, Sindi, Suzanne, Theis, Fabian J, Way, Gregory P, Yang, Jean YH, Fertig, Elana J

Subject Terms: Quantitative Biology - Other Quantitative Biology, Computer Science - Computers and Society

Access URL: http://arxiv.org/abs/2104.11364

Weakly Supervised Learning of Single-Cell Feature Embeddings

Authors: Caicedo, Juan C., McQuin, Claire, Goodman, Allen, Singh, Shantanu, Carpenter, Anne E.

Source: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition CVPR Computer Vision and Pattern Recognition (CVPR), 2018 IEEE/CVF Conference on. :9309-9318 Jun, 2018

Relation: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

Combining morphological and migration profiles of in vitro time-lapse data

Authors: Becker, Tim, Caicedo, Juan C., Singh, Shantanu, Weckmann, Markus, Carpenter, Anne E.

Source: 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) Biomedical Imaging (ISBI 2018), 2018 IEEE 15th International Symposium on. :965-968 Apr, 2018

Relation: 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018)

Deductive automated pollen classification in environmental samples via exploratory deep learning and imaging flow cytometry

Authors: Barnes, Claire M., Power, Ann L., Barber, Daniel G., Tennant, Richard K., Jones, Richard T., Lee, G. Rob, Hatton, Jackie, Elliott, Angela, Zaragoza‐Castells, Joana, Haley, Stephen M., Summers, Huw D., Doan, Minh, Carpenter, Anne E., Rees, Paul, Love, John

Source: New phytologist. 240(3):1305-1326

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100195094027.0x000001&indx=1&recIds=ETOCvdc_100195094027.0x000001

Integrating inflammatory biomarker analysis and artificial-intelligence-enabled image-based profiling to identify drug targets for intestinal fibrosis

Authors: Yu, Shan, Kalinin, Alexandr A., Paraskevopoulou, Maria D., Maruggi, Marco, Cheng, Jie, Tang, Jie, Icke, Ilknur, Luo, Yi, Wei, Qun, Scheibe, Dan, Hunter, Joel, Singh, Shantanu, Nguyen, Deborah, Carpenter, Anne E., Horman, Shane R.

Source: In Cell Chemical Biology 21 September 2023 30(9):1169-1182

Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler

Authors: Laber, Samantha, Strobel, Sophie, Mercader, Josep M., Dashti, Hesam, dos Santos, Felipe R.C., Kubitz, Phil, Jackson, Maya, Ainbinder, Alina, Honecker, Julius, Agrawal, Saaket, Garborcauskas, Garrett, Stirling, David R., Leong, Aaron, Figueroa, Katherine, Sinnott-Armstrong, Nasa, Kost-Alimova, Maria, Deodato, Giacomo, Harney, Alycen, Way, Gregory P., Saadat, Alham, Harken, Sierra, Reibe-Pal, Saskia, Ebert, Hannah, Zhang, Yixin, Calabuig-Navarro, Virtu, McGonagle, Elizabeth, Stefek, Adam, Dupuis, Josée, Cimini, Beth A., Hauner, Hans, Udler, Miriam S., Carpenter, Anne E., Florez, Jose C., Lindgren, Cecilia, Jacobs, Suzanne B.R., Claussnitzer, Melina

Source: In Cell Genomics 12 July 2023 3(7)

FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity

Authors: Wieder, Nicolas, Fried, Juliana Coraor, Kim, Choah, Sidhom, Eriene-Heidi, Brown, Matthew R., Marshall, Jamie L., Arevalo, Carlos, Dvela-Levitt, Moran, Kost-Alimova, Maria, Sieber, Jonas, Gabriel, Katlyn R., Pacheco, Julian, Clish, Clary, Abbasi, Hamdah Shafqat, Singh, Shantanu, Rutter, Justine C., Therrien, Martine, Yoon, Haejin, Lai, Zon Weng, Baublis, Aaron, Subramanian, Renuka, Devkota, Ranjan, Small, Jonnell, Sreekanth, Vedagopuram, Han, Myeonghoon, Lim, Donghyun, Carpenter, Anne E., Flannick, Jason, Finucane, Hilary, Haigis, Marcia C., Claussnitzer, Melina, Sheu, Eric, Stevens, Beth, Wagner, Bridget K., Choudhary, Amit, Shaw, Jillian L., Pablo, Juan Lorenzo, Greka, Anna

Source: In Cell Metabolism 2 May 2023 35(5):887-905

Symmetry-based mitosis detection in time-lapse microscopy

Authors: Gilad, Topaz, Bray, Mark-Anthony, Carpenter, Anne E., Raviv, Tammy Riklin

Source: 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI) Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on. :164-167 Apr, 2015

Relation: 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI 2015)

Applying Faster R-CNN for Object Detection on Malaria Images

Authors: Hung, Jane, Ravel, Deepali, Lopes, Stefanie C. P., Rangel, Gabriel, Nery, Odailton Amaral, Malleret, Benoit, Nosten, Francois, Lacerda, Marcus V. G., Ferreira, Marcelo U., Rénia, Laurent, Duraisingh, Manoj T., Costa, Fabio T. M., Marti, Matthias, Carpenter, Anne E.

Subject Terms: Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/1804.09548

Morphology and gene expression profiling provide complementary information for mapping cell state

Authors: Way, Gregory P., Natoli, Ted, Adeboye, Adeniyi, Litichevskiy, Lev, Yang, Andrew, Lu, Xiaodong, Caicedo, Juan C., Cimini, Beth A., Karhohs, Kyle, Logan, David J., Rohban, Mohammad H., Kost-Alimova, Maria, Hartland, Kate, Bornholdt, Michael, Chandrasekaran, Srinivas Niranj, Haghighi, Marzieh, Weisbart, Erin, Singh, Shantanu, Subramanian, Aravind, Carpenter, Anne E.

Source: In Cell Systems 16 November 2022 13(11):911-923

The new era of quantitative cell imaging—challenges and opportunities

Authors: Bagheri, Neda, Carpenter, Anne E., Lundberg, Emma, Plant, Anne L., Horwitz, Rick

Source: Molecular cell. 82(2):241-247

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100163420031.0x000001&indx=1&recIds=ETOCvdc_100163420031.0x000001

Virtual screening for small-molecule pathway regulators by image-profile matching

Authors: Rohban, Mohammad H., Fuller, Ashley M., Tan, Ceryl, Goldstein, Jonathan T., Syangtan, Deepsing, Gutnick, Amos, DeVine, Ann, Nijsure, Madhura P., Rigby, Megan, Sacher, Joshua R., Corsello, Steven M., Peppler, Grace B., Bogaczynska, Marta, Boghossian, Andrew, Ciotti, Gabrielle E., Hands, Allison T., Mekareeya, Aroonroj, Doan, Minh, Gale, Jennifer P., Derynck, Rik, Turbyville, Thomas, Boerckel, Joel D., Singh, Shantanu, Kiessling, Laura L., Schwarz, Thomas L., Varelas, Xaralabos, Wagner, Florence F., Kafri, Ran, Eisinger-Mathason, T.S. Karin, Carpenter, Anne E.

Source: In Cell Systems 21 September 2022 13(9):724-736