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S

Shantanu Singh

MIT and Harvard

43H-index
215Paper Count
9.7KCitation Count
Published Papers 53
Publication Date
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Progress and new challenges in image-based profiling
errMolecular Systems Biology
IF7.7
err2026-03-27
err0
errOAAI
errErik Serrano; John Peters; Jesko Wagner; Rebecca E Graham; Zhenghao Chen; Brian Y Feng; Gisele Miranda; Alexandr A Kalinin; Loan Vulliard; Jenna Tomkinson; Cameron Mattson; Michael J Lippincott; Ziqi Kang; Divya Sitani; Dave Bunten; Srijit Seal; Neil O Carragher; Anne E Carpenter; Shantanu Singh; Paula A Marin Zapata; Juan C Caicedo; Gregory P Way
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errSave
nELISA: a high-throughput, high-plex platform enables quantitative profiling of the inflammatory secretome
errNature Methods
IF32.1
err2025-11-07
err0
errOAAI
errMilad 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; Baly Sow; Michael Vrouvides; Andy Lee; Philippe DeCorwin-Martin; Shafqat Rasool; Jiamin Huang; Timothy Erps; Spencer Coffin; Narges M. Rashidi; Yu Han; Srinivas Niranj Chandrasekaran; Lisa Miller; Maria Kost-Alimova; Adam Skepner; Shantanu Singh; Anne E. Carpenter; Jeffrey D. Munzar; David Juncker
errShare
errSave
The OASIS Consortium: integrating multi-omics technologies to transform chemical safety assessment
errTOXICOLOGICAL SCIENCES
IF4.1
err2025-10-01
err0
errOAAI
errRouquie, David; Bender, Andreas; Cheah, Jaime; Crute, Christine E.; Dalmas, Deidre; Ewald, Jessica; Fullerton, Aaron; Harrill, Joshua A.; Kadri, Sabah; Kleinstreuer, Nicole; Kramer, Nynke; LaRocca, Jessica; Mitchell, Constance A.; Seal, Srijit; Singh, Shantanu; Carpenter, Anne E.
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errSave
Acquisition, quality control, and architecture of a large image dataset as a tool for in silico cell biological research
errMaterials Today Bio
IF10.2
err2025-09-24
err0
errOAAI
errNikita Konshin; Marta Garcia Valverde; Danila Solodennikov; Koen Minartz; Vlado Menkovski; Rosalinde Masereeuw; Shantanu Singh; Silvia M. Mihăilă; Jan de Boer
errShare
errSave
Alternate dyes for image-based profiling assays
errSLAS Discovery
IF2.7
err2025-08-28
err0
errOAAI
errSuganya Sivagurunathan; Patrick Byrne; Alán F. Muñoz; John Arevalo; Anne E. Carpenter; Shantanu Singh; Maria Kost-Alimova; Beth A. Cimini
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errSave
Combining phenomics with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion
errNature Communications
IF15.7
err2025-07-09
err0
errOAAI
errMatthew Tegtmeyer; Dhara Liyanage; Yu Han; Kathryn B. Hebert; Ruifan Pei; Gregory P. Way; Pearl V. Ryder; Derek Hawes; Callum Tromans-Coia; Beth A. Cimini; Anne E. Carpenter; Shantanu Singh; Ralda Nehme
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errSave
Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World
errCHEMICAL RESEARCH IN TOXICOLOGY
IF3.8
err2025-05-02
err0
errOAAI
errSeal, Srijit; Mahale, Manas; Garcia-Ortegon, Miguel; Joshi, Chaitanya K.; Hosseini-Gerami, Layla; Beatson, Alex; Greenig, Matthew; Shekhar, Mrinal; Patra, Arijit; Weis, Caroline; Mehrjou, Arash; Badre, Adrien; Paisley, Brianna; Lowe, Rhiannon; Singh, Shantanu; Shah, Falgun; Johannesson, Bjarki; Williams, Dominic; Rouquie, David; Clevert, Djork-Arne; Schwab, Patrick; Richmond, Nicola; Nicolaou, Christos A.; Gonzalez, Raymond J.; Naven, Russell; Schramm, Carolin; Vidler, Lewis R.; Mansouri, Kamel; Walters, W. Patrick; Wilk, Deidre Dalmas; Spjuth, Ola; Carpenter, Anne E.; Bender, Andreas
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errSave
Cell Painting: a decade of discovery and innovation in cellular imaging (Dec, 10.1038/s41592-024-02528-8, 2024)
errNATURE METHODS
IF32.1
err2024-12-12
err0
PREAI
errSeal, Srijit; Trapotsi, Maria-Anna; Spjuth, Ola; Singh, Shantanu; Carreras-Puigvert, Jordi; Greene, Nigel; Bender, Andreas; Carpenter, Anne E.
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errSave
Cell Painting: a decade of discovery and innovation in cellular imaging
errNATURE METHODS
IF32.1
err2024-12-05
err1
PREAI
errSeal, Srijit; Trapotsi, Maria-Anna; Spjuth, Ola; Singh, Shantanu; Carreras-Puigvert, Jordi; Greene, Nigel; Bender, Andreas; Carpenter, Anne E.
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errSave
Cell Painting Gallery: an open resource for image-based profiling
errNATURE METHODS
IF32.1
err2024-09-02
err0
PREAI
errWeisbart, Erin; Kumar, Ankur; Arevalo, John; Carpenter, Anne E.; Cimini, Beth A.; Singh, Shantanu
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errSave
Evaluating batch correction methods for image-based cell profiling
errNATURE COMMUNICATIONS
IF15.7
err2024-08-02
err1
errOAAI
errArevalo, John; Su, Ellen; Ewald, Jessica D.; Van Dijk, Robert; Carpenter, Anne E.; Singh, Shantanu
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errSave
Opting for polyamines with specific structural traits as a strategy to boost performance of enzymatic membrane reactors
errCHEMICAL ENGINEERING JOURNAL
IF13.2
err2024-08-01
err0
errOAAI
errPopkov, Andrei; Malankowska, Magdalena; De Martini, Markus Simon; Singh, Shantanu; Su, Ziran; Pinelo, Manuel
errShare
errSave
Development and validation of a high-throughput drug screen (HTDS) from patient-derived tumor organoids (PDTO) from gastrointestinal malignancies: Clinical and genomic correlations
errANNALS OF ONCOLOGY
IF65.4
err2024-06-01
err0
PREAI
errKhan, U.; Singh, S.; Us, I.; Sarkar, S.; Alban, T.; Chan, T.; Hissong, E.; Bhinder, B.; Moyer, J.; Martin, L.; Shah, M. A.
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errSave
Giant Modulation of Refractive Index from Picoscale Atomic Displacements
errADVANCED MATERIALS
IF26.8
err2024-04-10
err3
errOAAI
errZhao, Boyang; Ren, Guodong; Mei, Hongyan; Wu, Vincent C.; Singh, Shantanu; Jung, Gwan Yeong; Chen, Huandong; Giovine, Raynald; Niu, Shanyuan; Thind, Arashdeep S.; Salman, Jad; Settineri, Nick S.; Chakoumakos, Bryan C.; Manley, Michael E.; Hermann, Raphael P.; Lupini, Andrew R.; Chi, Miaofang; Hachtel, Jordan A.; Simonov, Arkadiy; Teat, Simon J.; Clement, Raphaele J.; Kats, Mikhail A.; Ravichandran, Jayakanth; Mishra, Rohan
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errSave
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
errNATURE METHODS
IF32.1
err2024-04-09
err10
errOAAI
errChandrasekaran, Srinivas Niranj; Cimini, Beth A.; Goodale, Amy; Miller, Lisa; Kost-Alimova, Maria; Jamali, Nasim; Doench, John G.; Fritchman, Briana; Skepner, Adam; Melanson, Michelle; Kalinin, Alexandr A.; Arevalo, John; Haghighi, Marzieh; Caicedo, Juan C.; Kuhn, Daniel; Hernandez, Desiree; Berstler, James; Shafqat-Abbasi, Hamdah; Root, David E.; Swalley, Susanne E.; Garg, Sakshi; Singh, Shantanu; Carpenter, Anne E.
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errSave
From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability
errMOLECULAR BIOLOGY OF THE CELL
IF2.7
err2024-03-01
err5
errOAAI
errSeal, Srijit; Carreras-Puigvert, Jordi; Singh, Shantanu; Carpenter, Anne E.; Spjuth, Ola; Bender, Andreas
errShare
errSave
Learning representations for image-based profiling of perturbations
errNATURE COMMUNICATIONS
IF15.7
err2024-02-21
err9
errOAAI
errMoshkov, Nikita; Bornholdt, Michael; Benoit, Santiago; Smith, Matthew; Mcquin, Claire; Goodman, Allen; Senft, Rebecca A.; Han, Yu; Babadi, Mehrtash; Horvath, Peter; Cimini, Beth A.; Carpenter, Anne E.; Singh, Shantanu; Caicedo, Juan C.
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errSave
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2024-02-01
err8
errOAAI
errSeal, Srijit; Spjuth, Ola; Hosseini-Gerami, Layla; Garcia-Ortegon, Miguel; Singh, Shantanu; Bender, Andreas; Carpenter, Anne E.
errShare
errSave
Bringing computation to biology by bridging the last mile
errNATURE CELL BIOLOGY
IF19.1
err2024-01-16
err2
errOAAI
errCarpenter, Anne E.; Singh, Shantanu
errShare
errSave
High-dimensional phenotyping to define the genetic basis of cellular morphology
errNATURE COMMUNICATIONS
IF15.7
err2024-01-06
err11
errOAAI
errTegtmeyer, Matthew; Arora, Jatin; Asgari, Samira; Cimini, Beth A.; Nadig, Ajay; Peirent, Emily; Liyanage, Dhara; Way, Gregory P.; Weisbart, Erin; Nathan, Aparna; Amariuta, Tiffany; Eggan, Kevin; Haghighi, Marzieh; Mccarroll, Steven A.; O'Connor, Luke; Carpenter, Anne E.; Singh, Shantanu; Nehme, Ralda; Raychaudhuri, Soumya
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errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
R
Ramnik J. Xavier
H-index: 186 · Papers: 999
T
Todd R. Golub
H-index: 176 · Papers: 749
S
Stuart L. Schreiber
H-index: 166 · Papers: 1.3K
W
William C. Hahn
H-index: 147 · Papers: 1.1K
C
Clary B. Clish
H-index: 141 · Papers: 1.0K
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