9 citations · 23 across the 11 of their papers we have counts for
11 papers
JUMP-lite: Compact, reproducible benchmarking of cell representations
Alán F. Muñoz, Johan Fredin Haslum, Runxi Shen +2
Image-based profiling captures rich phenotypic signatures for drug discovery and functional genomics. Large public datasets like JUMP Cell Painting now provide millions of images f…
Science sandboxes measure the scientific capability of AI agents
Arya S. Rao, Rodrigo I. Castro, Sager J. Gosai +8
Scientific progress depends not only on finding solutions, but on learning the rules that explain why they work and using that understanding to design better experiments. We introd…
cubic: CUDA-accelerated 3D Bioimage Computing
Alexandr A. Kalinin, Anne E. Carpenter, Shantanu Singh +1
Quantitative analysis of multidimensional biological images is useful for understanding complex cellular phenotypes and accelerating advances in biomedical research. As modern micr…
Progress and new challenges in image-based profiling
Erik Serrano, John Peters, Jesko Wagner +19
For over two decades, image-based profiling has revolutionized cell phenotype analysis. Image-based profiling processes rich, high-throughput, microscopy data into thousands of unb…
Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling
Alexandr A. Kalinin, Paula Llanos, Theresa Maria Sommer +11
Microscopy enables direct observation of cellular morphology in 3D, with transmitted-light methods offering low-cost, minimally invasive imaging and fluorescence microscopy providi…
cp_measure: API-first feature extraction for image-based profiling workflows
Alán F. Muñoz, Tim Treis, Alexandr A. Kalinin +4
Biological image analysis has traditionally focused on measuring specific visual properties of interest for cells or other entities. A complementary paradigm gaining increasing tra…
Numerical and Lyapunov-Based Investigation of the Effect of Stenosis on Blood Transport Stability Using a Control-Theoretic PDE Model of Cardiovascular Flow
Shantanu Singh, Nikolaos Bekiaris-Liberis
We perform various numerical tests to study the effect of (boundary) stenosis on blood flow stability, employing a detailed and accurate, second-order finite-volume scheme for nume…
Learning Molecular Representation in a Cell
Gang Liu, Srijit Seal, John Arevalo +4
Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, curre…
MOTIVE: A Drug-Target Interaction Graph For Inductive Link Prediction
John Arevalo, Ellen Su, Anne E Carpenter +1
Drug-target interaction (DTI) prediction is crucial for identifying new therapeutics and detecting mechanisms of action. While structure-based methods accurately model physical int…
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting
Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth +5
High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism o…
Understanding Biology in the Age of Artificial Intelligence
Elsa Lawrence, Adham El-Shazly, Srijit Seal +6
Modern life sciences research is increasingly relying on artificial intelligence approaches to model biological systems, primarily centered around the use of machine learning (ML)…