413 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- The Ohio State UniversityUS17 papers
- BattelleUS12 papers
- Stanford UniversityUS3 papers
- Beth Israel Deaconess Medical CenterUS2 papers
- Boston Children's HospitalUS2 papers
- Children's Hospital of PhiladelphiaUS2 papers
- Cornell UniversityUS2 papers
- Emory UniversityUS2 papers
- Harvard UniversityUS2 papers
- Wake Forest UniversityUS2 papers
- Yale UniversityUS2 papers
- All India Institute of Medical Sciences RishikeshIN1 paper
29 papers
Zero-shot generation of synthetic neurosurgical data with large language models
Austin A. Barr, Eddie Guo, Emre Sezgin
Clinical data is fundamental to advance neurosurgical research, but access is often constrained by data availability, small sample sizes, privacy regulations, and resource-intensiv…
BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 2023
Anahita Fathi Kazerooni, Nastaran Khalili, Xinyang Liu +77
Pediatric central nervous system tumors are the leading cause of cancer-related deaths in children. The five-year survival rate for high-grade glioma in children is less than 20%.…
A Fluid-Solid-Growth Solver for Cardiovascular Modeling
Erica L. Schwarz, Martin R. Pfaller, Jason M. Szafron +5
We implement full, three-dimensional constrained mixture theory for vascular growth and remodeling into a finite element fluid-structure interaction (FSI) solver. The resulting "fl…
Deep Learning Pipeline for Preprocessing and Segmenting Cardiac Magnetic Resonance of Single Ventricle Patients from an Image Registry
Tina Yao, Nicole St. Clair, Gabriel F. Miller +13
Purpose: To develop and evaluate an end-to-end deep learning pipeline for segmentation and analysis of cardiac magnetic resonance images to provide core-lab processing for a multi-…
Determining clinically relevant features in cytometry data using persistent homology
Soham Mukherjee, Darren Wethington, Tamal K. Dey +1
Cytometry experiments yield high-dimensional point cloud data that is difficult to interpret manually. Boolean gating techniques coupled with comparisons of relative abundances of…
A Simple Standard for Sharing Ontological Mappings (SSSOM)
Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello +41
Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representatio…
Transformer-based unsupervised patient representation learning based on medical claims for risk stratification and analysis
Xianlong Zeng, Simon Lin, Chang Liu
The claims data, containing medical codes, services information, and incurred expenditure, can be a good resource for estimating an individual's health condition and medical risk l…
A Large Collection of Real-world Pediatric Sleep Studies
Harlin Lee, Boyue Li, Shelly DeForte +4
Despite being crucial to health and quality of life, sleep -- especially pediatric sleep -- is not yet well understood. This is exacerbated by lack of access to sufficient pediatri…
An integrated abundance model for estimating county-level prevalence of opioid misuse in Ohio
Staci A. Hepler, David Kline, Andrea Bonny +2
Opioid misuse is a national epidemic and a significant drug related threat to the United States. While the scale of the problem is undeniable, estimates of the local prevalence of…
Little Motion, Big Results: Using Motion Magnification to Reveal Subtle Tremors in Infants
Girik Malik, Ish K. Gulati
Detecting tremors is challenging for both humans and machines. Infants exposed to opioids during pregnancy often show signs and symptoms of withdrawal after birth, which are easy t…
SurfCon: Synonym Discovery on Privacy-Aware Clinical Data
Zhen Wang, Xiang Yue, Soheil Moosavinasab +3
Unstructured clinical texts contain rich health-related information. To better utilize the knowledge buried in clinical texts, discovering synonyms for a medical query term has bec…
Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations
Xiang Yue, Zhen Wang, Jingong Huang +7
Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding…
Probing Time-Dependent Dark Energy with the Flux Power Spectrum of the Lyman Forest
Jared W. Coughlin, Grant J. Mathews, Lara Arielle Phillips +2
We present new simulations of the flux power spectrum of the Lyman forest as a means to investigate the effects of time-dependent dark energy on structure formation. We use a l…
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes
Maksim Kouza, Anirban Banerji, Andrzej Kolinski +2
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical resear…
Absolutely Zero Evidence
Veronica J. Vieland
Statistical analysis is often used to evaluate the evidence for or against scientific hypotheses, and various statistics (e.g., p-values, likelihood ratios, Bayes factors) are inte…
Yarkovsky Drift Detections for 247 Near-Earth Asteroids
Adam H. Greenberg, Jean-Luc Margot, Ashok K. Verma +2
The Yarkovsky effect is a thermal process acting upon the orbits of small celestial bodies, which can cause these orbits to slowly expand or contract with time. The effect is subtl…
Statistical Evidence Measured on a Properly Calibrated Scale Across Nested and Non-nested Hypothesis Comparisons
V. J Vieland, S-C. Seok
Statistical modeling is often used to measure the strength of evidence for or against hypotheses on given data. We have previously proposed an information-dynamic framework in supp…
Limiting energy dissipation induces glassy kinetics in single cell high precision responses
Jayajit Das
Single cells often generate precise responses by involving dissipative out-of-thermodynamic equilibrium processes in signaling networks. The available free energy to fuel these pro…
Maximum Entropy estimation of probability distribution of variables in higher dimensions from lower dimensional data
Jayajit Das, Sayak Mukherjee, Susan E. Hodge
A common statistical situation concerns inferring an unknown distribution Q(x) from a known distribution P(y), where X (dimension n), and Y (dimension m) have a known functional re…
Addressing the unmet need for visualizing Conditional Random Fields in Biological Data
William C. Ray, Samuel L. Wolock, Nicholas W Callahan +5
Background: The biological world is replete with phenomena that appear to be ideally modeled and analyzed by one archetypal statistical framework - the Graphical Probabilistic Mode…
Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures
Sarah A. Munro, Steve P. Lund, P. Scott Pine +30
There is a critical need for standard approaches to assess, report, and compare the technical performance of genome-scale differential gene expression experiments. We assess techni…
Host-to-host variation of ecological interactions in polymicrobial infections
Sayak Mukherjee, Kristin E. Weimer, Sang-Cheol Seok +5
Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of…
In silico Modeling of Itk Activation Kinetics in Thymocytes Suggests Competing Positive and Negative IP4 Mediated Feedbacks Increase Robustness
Sayak Mukherjee, Stephanie Rigaud, Sang-Cheol Seok +7
The inositol-phosphate messenger inositol(1,3,4,5)tetrakisphosphate (IP4) is essential for thymocyte positive selection by regulating plasma-membrane association of the protein tyr…
Cell responses only partially shape cell-to-cell variations in protein abundances in Escherichia coli chemotaxis
Sayak Mukherjee, Sang-Cheol Seok, Veronica J. Vieland +1
Cell-to-cell variations in protein abundance in clonal cell populations are ubiquitous in living systems. Since protein composition determines responses in individual cells, it sta…