Shantanu Singh (S Singh)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 62

Top Topics

Top Venues

Nature communications

bioRxiv : the preprint server for biology

Nature cell biology

Molecular biology of the cell

This page only lists publications with an associated author ORCID identifier.

Publications

Anne E Carpenter, Shantanu Singh
Bringing computation to biology by bridging the last mile. Nature cell biology 26 (1) (2024)
Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E Carpenter
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. bioRxiv : the preprint server for biology (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Anne E Carpenter, Shantanu Singh
Bringing computation to biology by bridging the last mile. Nature cell biology 26 (1) (2024)
Srijit Seal, Jordi Carreras-Puigvert, Shantanu Singh, Anne E Carpenter, Ola Spjuth, Andreas Bender
From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability. Molecular biology of the cell 35 (3) (2024)
Alexandr A Kalinin, John Arevalo, Loan Vulliard, Erik Serrano, Hillary Tsang, Michael Bornholdt, Bartek Rajwa, Anne E Carpenter, Gregory P Way, Shantanu Singh
A versatile information retrieval framework for evaluating profile strength and similarity. bioRxiv : the preprint server for biology (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Udit Surya Saha, Christopher M Dobson, Anne E Carpenter, Shantanu Singh, Andreas Bender, Srijit Seal
Step Forward Cross Validation for Bioactivity Prediction: Out of Distribution Validation in Drug Discovery. bioRxiv : the preprint server for biology (2024)
Srijit Seal, Jordi Carreras-Puigvert, Shantanu Singh, Anne E Carpenter, Ola Spjuth, Andreas Bender
From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability. Molecular biology of the cell 35 (3) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Robert H W 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. bioRxiv : the preprint server for biology (2024)
Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Juan C Caicedo
Learning representations for image-based profiling of perturbations. Nature communications 15 (1) (2024)
Anne E Carpenter, Shantanu Singh
Bringing computation to biology by bridging the last mile. Nature cell biology 26 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Anne E Carpenter, Shantanu Singh
Bringing computation to biology by bridging the last mile. Nature cell biology 26 (1) (2024)
Alexandr A Kalinin, John Arevalo, Loan Vulliard, Erik Serrano, Hillary Tsang, Michael Bornholdt, Bartek Rajwa, Anne E Carpenter, Gregory P Way, Shantanu Singh
A versatile information retrieval framework for evaluating profile strength and similarity. bioRxiv : the preprint server for biology (2024)
Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Juan C Caicedo
Learning representations for image-based profiling of perturbations. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E Carpenter
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. bioRxiv : the preprint server for biology (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Srijit Seal, Jordi Carreras-Puigvert, Shantanu Singh, Anne E Carpenter, Ola Spjuth, Andreas Bender
From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability. Molecular biology of the cell 35 (3) (2024)
Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E Carpenter
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. bioRxiv : the preprint server for biology (2024)
Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Juan C Caicedo
Learning representations for image-based profiling of perturbations. Nature communications 15 (1) (2024)
Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Juan C Caicedo
Learning representations for image-based profiling of perturbations. Nature communications 15 (1) (2024)
Srijit Seal, Jordi Carreras-Puigvert, Shantanu Singh, Anne E Carpenter, Ola Spjuth, Andreas Bender
From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability. Molecular biology of the cell 35 (3) (2024)
John Arevalo, Ellen Su, Jessica D Ewald, Robert van Dijk, Anne E Carpenter, Shantanu Singh
Evaluating batch correction methods for image-based cell profiling. Nature communications 15 (1) (2024)
Alexandr A Kalinin, John Arevalo, Loan Vulliard, Erik Serrano, Hillary Tsang, Michael Bornholdt, Bartek Rajwa, Anne E Carpenter, Gregory P Way, Shantanu Singh
A versatile information retrieval framework for evaluating profile strength and similarity. bioRxiv : the preprint server for biology (2024)
Udit Surya Saha, Christopher M Dobson, Anne E Carpenter, Shantanu Singh, Andreas Bender, Srijit Seal
Step Forward Cross Validation for Bioactivity Prediction: Out of Distribution Validation in Drug Discovery. bioRxiv : the preprint server for biology (2024)
Srijit Seal, Jordi Carreras-Puigvert, Shantanu Singh, Anne E Carpenter, Ola Spjuth, Andreas Bender
From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability. Molecular biology of the cell 35 (3) (2024)
Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E Carpenter
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. bioRxiv : the preprint server for biology (2024)
John Arevalo, Ellen Su, Jessica D Ewald, Robert van Dijk, Anne E Carpenter, Shantanu Singh
Evaluating batch correction methods for image-based cell profiling. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Erin Weisbart, Ankur Kumar, John Arevalo, Anne E Carpenter, Beth A Cimini, Shantanu Singh
Cell Painting Gallery: an open resource for image-based profiling. Nature methods (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
John Arevalo, Ellen Su, Jessica D Ewald, Robert van Dijk, Anne E Carpenter, Shantanu Singh
Evaluating batch correction methods for image-based cell profiling. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Robert H W 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. bioRxiv : the preprint server for biology (2024)
Anne E Carpenter, Shantanu Singh
Bringing computation to biology by bridging the last mile. Nature cell biology 26 (1) (2024)
Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Juan C Caicedo
Learning representations for image-based profiling of perturbations. Nature communications 15 (1) (2024)
Jayme L Dahlin, Bruce K Hua, Beth E Zucconi, Shawn D Nelson, Shantanu Singh, Anne E Carpenter, Jonathan H Shrimp, Evelyne Lima-Fernandes, Mathias J Wawer, Lawrence P W Chung, Ayushi Agrawal, Mary O'Reilly, Dalia Barsyte-Lovejoy, Magdalena Szewczyk, Fengling Li, Parnian Lak, Matthew E Cuellar, Philip A Cole, Jordan L Meier, Tim Thomas, Jonathan B Baell, Peter J Brown, Michael A Walters, Paul A Clemons, Stuart L Schreiber, Bridget K Wagner
Reference compounds for characterizing cellular injury in high-content cellular morphology assays. Nature communications 14 (1) (2023)
Jayme L Dahlin, Bruce K Hua, Beth E Zucconi, Shawn D Nelson, Shantanu Singh, Anne E Carpenter, Jonathan H Shrimp, Evelyne Lima-Fernandes, Mathias J Wawer, Lawrence P W Chung, Ayushi Agrawal, Mary O'Reilly, Dalia Barsyte-Lovejoy, Magdalena Szewczyk, Fengling Li, Parnian Lak, Matthew E Cuellar, Philip A Cole, Jordan L Meier, Tim Thomas, Jonathan B Baell, Peter J Brown, Michael A Walters, Paul A Clemons, Stuart L Schreiber, Bridget K Wagner
Reference compounds for characterizing cellular injury in high-content cellular morphology assays. Nature communications 14 (1) (2023)
Meraj Ramezani, Julia R Bauman, Avtar Singh, Erin Weisbart, John Yong, Maria Lozada, Gregory P Way, Sanam L Kavari, Celeste Diaz, Marzieh Haghighi, Thiago Martins Batista, Joaquín Pérez-Schindler, Melina Claussnitzer, Shantanu Singh, Beth A Cimini, Paul C Blainey, Anne E Carpenter, Calvin H Jan, James T Neal
A genome-wide atlas of human cell morphology. bioRxiv : the preprint server for biology (2023)
Milad Dagher, Grant Ongo, Nathaniel Robichaud, Jinglin Kong, Woojong Rho, Ivan Teahulos, Arya Tavakoli, Samantha Bovaird, Shahem Merjaneh, Andrew Tan, Kiran Edwardson, Christelle Scheepers, Andy Ng, Andy Hajjar, Andy Lee, Philippe DeCorwin-Martin, Shafqat Rasool, JiaMin Huang, Yu Han, Srinivas Niranj Chandrasekaran, Lisa Miller, Maria Kost-Alimova, Adam Skepner, Shantanu Singh, Jeffrey Munzar, Anne E Carpenter, David Juncker
nELISA: A high-throughput, high-plex platform enables quantitative profiling of the secretome. bioRxiv : the preprint server for biology (2023)
Megan E Kelley, Adi Y Berman, David R Stirling, Beth A Cimini, Yu Han, Shantanu Singh, Anne E Carpenter, Tarun M Kapoor, Gregory P Way
High-content microscopy reveals a morphological signature of bortezomib resistance. bioRxiv : the preprint server for biology (2023)
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 DICTrank. bioRxiv : the preprint server for biology (2023)
Megan E Kelley, Adi Y Berman, David R Stirling, Beth A Cimini, Yu Han, Shantanu Singh, Anne E Carpenter, Tarun M Kapoor, Gregory P Way
High-content microscopy reveals a morphological signature of bortezomib resistance. bioRxiv : the preprint server for biology (2023)
Jayme L Dahlin, Bruce K Hua, Beth E Zucconi, Shawn D Nelson, Shantanu Singh, Anne E Carpenter, Jonathan H Shrimp, Evelyne Lima-Fernandes, Mathias J Wawer, Lawrence P W Chung, Ayushi Agrawal, Mary O'Reilly, Dalia Barsyte-Lovejoy, Magdalena Szewczyk, Fengling Li, Parnian Lak, Matthew E Cuellar, Philip A Cole, Jordan L Meier, Tim Thomas, Jonathan B Baell, Peter J Brown, Michael A Walters, Paul A Clemons, Stuart L Schreiber, Bridget K Wagner
Reference compounds for characterizing cellular injury in high-content cellular morphology assays. Nature communications 14 (1) (2023)
Nikita Moshkov, Tim Becker, Kevin Yang, Peter Horvath, Vlado Dancik, Bridget K Wagner, Paul A Clemons, Shantanu Singh, Anne E Carpenter, Juan C Caicedo
Predicting compound activity from phenotypic profiles and chemical structures. Nature communications 14 (1) (2023)
Milad Dagher, Grant Ongo, Nathaniel Robichaud, Jinglin Kong, Woojong Rho, Ivan Teahulos, Arya Tavakoli, Samantha Bovaird, Shahem Merjaneh, Andrew Tan, Kiran Edwardson, Christelle Scheepers, Andy Ng, Andy Hajjar, Andy Lee, Philippe DeCorwin-Martin, Shafqat Rasool, JiaMin Huang, Yu Han, Srinivas Niranj Chandrasekaran, Lisa Miller, Maria Kost-Alimova, Adam Skepner, Shantanu Singh, Jeffrey Munzar, Anne E Carpenter, David Juncker
nELISA: A high-throughput, high-plex platform enables quantitative profiling of the secretome. bioRxiv : the preprint server for biology (2023)
Beth A Cimini, Srinivas Niranj Chandrasekaran, Maria Kost-Alimova, Lisa Miller, Amy Goodale, Briana Fritchman, Patrick Byrne, Sakshi Garg, Nasim Jamali, David J Logan, John B Concannon, Charles-Hugues Lardeau, Elizabeth Mouchet, Shantanu Singh, Hamdah Shafqat Abbasi, Peter Aspesi, Justin D Boyd, Tamara Gilbert, David Gnutt, Santosh Hariharan, Desiree Hernandez, Gisela Hormel, Karolina Juhani, Michelle Melanson, Lewis H Mervin, Tiziana Monteverde, James E Pilling, Adam Skepner, Susanne E Swalley, Anita Vrcic, Erin Weisbart, Guy Williams, Shan Yu, Bolek Zapiec, Anne E Carpenter
Optimizing the Cell Painting assay for image-based profiling. Nature protocols (2023)
John Arevalo, Robert van Dijk, Anne E Carpenter, Shantanu Singh
Evaluating batch correction methods for image-based cell profiling. bioRxiv : the preprint server for biology (2023)
Megan E Kelley, Adi Y Berman, David R Stirling, Beth A Cimini, Yu Han, Shantanu Singh, Anne E Carpenter, Tarun M Kapoor, Gregory P Way
High-content microscopy reveals a morphological signature of bortezomib resistance. eLife 12 (2023)
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 computational biology 18 (2) (2022)
Marzieh Haghighi, Juan C Caicedo, Beth A Cimini, Anne E Carpenter, Shantanu Singh
High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations. Nature methods 19 (12) (2022)
Eric Danielson, Karen Perez de Arce, Beth A Cimini, Eike-Christian Wamhoff, Shantanu Singh, Jeffrey R Cottrell, Anne E Carpenter, Mark Bathe
Molecular Diversity of Glutamatergic and GABAergic Synapses from Multiplexed Fluorescence Imaging. eNeuro 8 (1) (2021)
Minh Doan, Marian Case, Dino Masic, Holger Hennig, Claire McQuin, Juan Caicedo, Shantanu Singh, Allen Goodman, Olaf Wolkenhauer, Huw D Summers, David Jamieson, Frederik V Delft, Andrew Filby, Anne E Carpenter, Paul Rees, Julie Irving
Label-Free Leukemia Monitoring by Computer Vision. Cytometry. Part A : the journal of the International Society for Analytical Cytology 97 (4) (2020)
Mohammad H Rohban, Hamdah S Abbasi, Shantanu Singh, Anne E Carpenter
Capturing single-cell heterogeneity via data fusion improves image-based profiling. Nature communications 10 (1) (2019)
Juan C Caicedo, Allen Goodman, Kyle W Karhohs, Beth A Cimini, Jeanelle Ackerman, Marzieh Haghighi, CherKeng Heng, Tim Becker, Minh Doan, Claire McQuin, Mohammad Rohban, Shantanu Singh, Anne E Carpenter
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl. Nature methods 16 (12) (2019)
Juan C Caicedo, Jonathan Roth, Allen Goodman, Tim Becker, Kyle W Karhohs, Matthieu Broisin, Csaba Molnar, Claire McQuin, Shantanu Singh, Fabian J Theis, Anne E Carpenter
Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images. Cytometry. Part A : the journal of the International Society for Analytical Cytology 95 (9) (2019)
Mohammad Hossein Rohban, Shantanu Singh, Xiaoyun Wu, Julia B Berthet, Mark-Anthony Bray, Yashaswi Shrestha, Xaralabos Varelas, Jesse S Boehm, Anne E Carpenter
Systematic morphological profiling of human gene and allele function via Cell Painting. eLife 6 (2017)