Bioinformatics, Computational and Systems Biology

(A-13) The Chimera Algorithm, a 3-Dimensional Nuclear Segmentation Model, Accurately Segments Highly Overlapping Nuclei from Confocal Images

(A-12) Ensemble U-Net Architecture for Nuclei Segmentation with Novel dataset

(A-11) Structural Dynamics and Function of Hepcidin In the Context of Haemochromatosis Using AlphaFold2 and VMD.

(A-10) Predicting the Effects of Drugs on Commensal Bacteria with Machine Learning

(A-6) Support Vector Machine vs Convolutional Neural Network for Classification of Single Cancerous Extracellular Vesicles spectral signals

(A-5) Predicting ICU death and readmission risks using publicly available dataset

(A-8) Using Smart Imaging of Micrographs Process and Labeling for Integrated Image Screening and Analysis.

(A-9) Spatially resolved 3D gene neighborhood networks for prediction of immunomodulatory potential of mesenchymal stem cells

(A-7) RNA-seq analysis of gene modulation using ultrasound stimulation

(A-2) Uterine contraction detection using multi-scale sliding window Gaussian mixed model.

(A-3) Transcription factor localization dynamics and DNA binding drive distinct promoter interpretations

(A-1) SUPERLEGO - AI-driven minimal scaffold design to stabilize individual domains extracted from multidomain proteins

(A-4) Transcriptomic analysis suggests biological processes are shared among highly migratory cancer cells but accomplished through unique transcriptional programs

(A-38) Investigating the Impact of Intrinsic and Extrinsic Cell Properties on Apoptotic Signaling in Tumor Cells Using an ODE model

(A-40) Machine learning models for sequence-based prediction of the aggregation and solubility of therapeutic proteins and peptides

(A-39) Evolving genome-scale metabolic models to match experimental data

(A-32) Robustness Evaluation Procedure for Deep Medical Imaging Classifiers

(A-34) From systems to pathogenesis: zooming into molecular mechanisms of Zika virus replication and neuropathogenesis.

(A-33) Profiling Neuron Inflammation Driven by Alzheimer’s Disease and Type 2 Diabetes Associated Metabolites

(A-36) Preclinical Side Effect Prediction through Pathway Engineering of Protein Interaction Network Models

(A-35) Ranking Computational Model Parameters by Information Gained from Data Facilitates Searching for Evidence of Alternative Biological Hypotheses

(A-37) Patient-specific deep offline artificial pancreas for blood glucose regulation in type 1 diabetes

(A-15) The estimation of size and location of myocardial infarction using deep learning approach.

(A-16) Structure-based Prediction of Kinase Activation Amidst a Varied Mutational Landscape Using Privileged Learning

(A-17) Quantitative Assessment of Mitochondrial Function in Lungs of Rats Susceptible to Hyperoxia-Induced Acute Respiratory Distress Syndrome (ARDS)

(A-18) Reduced Order Modeling of an Aortic Hemodynamic Fingerprint in the Penn Medicine Biobank

(A-22) Validation of Photostimulatory Responses in Islet Cells Using Computer Vision Algorithms

(A-25) The role of active and passive mechanisms in cancer cell migration: combining multiscale simulations and 3D cultures

(A-23) Profiling the Neuroimmune Cascade in 3xTg Mice Exposed to Successive Mild Traumatic Brain Injuries

(A-19) The Perilous Effect of Concentrated Energy Dissipation during Acinar Recruitment

(A-31) VEGF/PDGF cross family heterodimerization: A new paradigm to growth factor signaling with significance in health and disease.

(A-27) Unsupervised Nuclei and Cell Segmentation in Multiplexed Images of Complex Tissue Samples

(A-26) Stem cells within the Stromal Vascular Fraction Differentiate Towards an Osteogenic Lineage on Apatite-Based Materials

(A-30) Stochastic Modeling of T Cell Killing in Melanoma

(B-62) Interleukins, Keratins, and Homeobox genes are differentially expressed around Keratin-Coated Percutaneous Devices

(B-57) Optimizing neutralizing antibodies and therapeutic immunization in HIV-1

(B-51) Multiple feedback loops drive oscillations and insulin resistance in the Insulin Receptor Signaling Pathway

(B-54) Identifying Liver Transplantation Rejection Mechanisms by Integration of Pre- and Post-Operative Donor and Recipient Immunologic Features

(B-55) Investigating Functional Hyperemia in Mouse Brain: A Systems Biology Perspective

(B-56) Metabolic modeling of sex-specific liver tissue suggests mechanisms of differences in toxicological responses

(B-63) Error neurons in supplementary eye field drive low-frequency cortical rhythmicity with a negligible contribution to current sources

(A-1) A mathematical model to assess obstructive sleep apnea severity

(A-1) Computational modeling of replication efficiency and late protein synthesis variabilities in HCMV-infected ARPE19 cells

(A-1) Tumor MHC class I Expression Levels Correlate with Altered Immune Cell Colocalization in Non-Small Cell Lung Cancer Tumor Microenvironment

(B-58) Interpretable and scalable integration of single-cell transcriptomics across conditions with PARAFAC2

(B-59) Mechanistic computational modeling of sFLT1 secretion in endothelial cells

(B-60) Mechanistic Computational Modeling of IL-2 and IL-2 Immunocytokines

(B-48) Morphological similarity measure for better tumor tissue sampling

(B-47) Highly Sensitive Spatial Omics Sequencing of Formalin-Fixed Paraffin-Embedded Tissue

(B-45) Metabolic response to platinum-based therapies in tumor spheroids and patient-derived organoids measured with Raman spectroscopy

(B-46) Oxygen Saturation effect on Respiratory Regulation

(B-49) High Throughput, Translational Dynamics in Single Cell Signaling

(M-517) Inhibition of p38 MAPK Phosphor-signaling Ameliorates Cytokine Correlated Depressive-like Behavioral Induced by Repetitive Mild Traumatic Brain Injury

(B-43) Multimodal Analysis of the Glioblastoma Tumor Microenvironment

(B-42) Improving outcome predictions for ovarian cancer through use of ordinal loss functions

(B-41) Model guided design of a biological controller for septic wound healing regulation.

(B-74) CRISPR-based keyword search in DNA memory

(B-73) Detailed Survey of an in-vitro Intestinal Epithelium Model by Single-Cell Transcriptomics

(A-24) Spatial morpho proteomics analysis in lymphoid follicles

(B-75) Diffusion Probabilistic Modeling for Rapid Assessment of T-cell Receptor Specificity

(B-76) Enabling Large-Scale Three-Dimensional Models of the Adaptive Immune Response

(B-77) Characterization of functional diversity of Pseudomonas aeruginosa clinical isolates with broadly representative phenotypes

(A-20) Rapid Electroporation-Dependent Tissue Property Prediction in Canine Lung Tumors

(A-21) Rapid assembly and characterization of a combinatorial toolkit for controlling gene expression in understudied bacteria.

(A-14) Physiologically-based pharmacokinetic computational modeling of sodium fluorescein blood clearance for the assessment of the degree of hepatic ischemia-reperfusion injury

(A-29) Predicted Regulatory Effects of Gut Microbiome on Estrogen Receptor Beta Signaling in Ulcerative Colitis by Supervised LIVE Modeling

(B-44) PepGPT: De novo Design of Target-Specific Peptides for Programmable Proteome Editing

(B-80) Characterizing Vaginal Microbiome Regulation of Progesterone Receptor Expression via Secondary Analysis of Host and Microbiome Multi-omics Data

(B-78) Comparative Analysis of Machine Learning & Transfer Learning for Personalized Therapy: Assessing Dll4 Heterogeneity in Triple-Negative Breast Cancer via Dynamic Enhanced Near-Infrared Imaging

(B-52) Leveraging Transfer Learning for Dll4 Expression Assessment in Triple-Negative Breast Cancer: A dynamic enhanced near-infrared Fluorescence Imaging Approach with Time-Series Image Representations

(B-53) Molecular Dynamics Simulations of Glucose Oxidase Reveal Alternate Dimer Forms with Potential for Better Direct Electron Transfer to Electrode Surfaces

(B-61) Machine Learning for the Design of Functional Formulations

(B-70) Deciphering the immune microenvironment and the stromal network in lymphoid tissues using highly multiplexed, spatially resolved imaging mass cytometry.

(C-81) A Large-Scale Characterization of AI Drug Development Companies

(A-28) Simulating Signaling Dynamics in Chimeric Antigen Receptor T-cells

(C-82) An Application of Complex Modeling in Biology: Studying Mechanochemical Dependence of Intracellular Entry Efficiency

(B-79) Computer Vision Pipeline for Automated Analysis of Poloxamer 188 Treatment of bTBI

(B-64) Identification of Key Feature Genes in Rheumatoid Arthritis Using Machine Learning and Analysis of Their Relationship with Immune Infiltration

(B-68) Emulating spatio-temporal dynamics of multi-cellular and multi-scale systems proves challenging with machine learning

(B-65) A Double-Edged Sword; The Enigmatic Role of Hybrid Helper T-cells in Mediating Anti-Tumor Immunity

(B-66) Capturing Spatiotemporal Signaling Patterns in Cellular Data with Geometric Scattering Trajectory Homology

(B-67) Efficient optimization of transformation protocols for oral streptococci using response surface methodology

(B-69) A data-driven approach to identify emergent behaviors of immune cells within germinal centers

(B-71) Dysregulation of the Normal Wound Healing Cascade in Volumetric Muscle Loss Injury

(A-2) BioModME for Building and Simulating Dynamic Computational Models of Complex Biological Networks

(A-2) Engineering prediction systems to characterize virus-host protein interactions for pandemic risk assessment

(A-3) Integration of Blood Cytokine Levels and Medical Record Data for Predicting Pelvic Organ Prolapse Surgical Outcome

(A-3) Integrative Model of Astrocyte-Mediated Neurovascular Coupling

(A-4) Construction of an effective model for engineered microbial dynamics against complex background microbiome

(A-5) Multiscale Modeling of BMP Signaling Pathway during Zebrafish Embryogenesis

(A-6) Mutation and spatial transcriptomic profiling reveal the tumor heterogeneity of breast cancer.

(A-7) Developing novel geospatial metrics to evaluate the tumor immune microenvironment

(A-8) TransCompR: Translatable Components Regression Reveals Human Sepsis Mechanisms through Mouse-Derived Gene Expression Patterns

(A-9) A computational model to understand the role of calcium activity in the zebrafish tailfin wound healing process.

(A-10) MATHEMATICAL MODELING OF IMMUNE RESPONSE TO SARS-CoV-2.

(A-12) Three-Dimensional Mapping of Coronary Vasculature Geometries

(A-13) Building Genetic Circuits to Control Bacterial Growth Location

(A-14) NF-κB Dynamics in Response to Dual Stimulation

(A-15) A novel molecular model for the identification of nanoparticle forming drug-excipient pairs

(A-16) Development of Machine Learning-Based Methods for Deep Behavioral Phenotyping during Sustain Attention Tasks in Mice

(A-17) A Novel Color Deconvolution Method with open source software for Accurate Visualization of Tissue Component

(A-18) Finding Monoamine Interacting Proteins in Micrococcus luteus for Use in Biosensors

(A-19) Mitochondrial Changes normalized with Transcriptome/Proteomic data in both Endurance and Sedentary subjects

(A-20) Systems Analysis of Beta-Blocker Activation of Cardiomyocyte Proliferation

(A-21) Sequence Patterning, Morphology, and Dispersity in Single-Chain Nanoparticles: Insights from Simulation and Machine Learning

(A-22) A Mathematical Model of Electrophysiology and Calcium Dynamics in Cerebral Artery Endothelial Cells

(A-23) Inferring the role of AP-1 protein dimerization in melanoma differentiation state heterogeneity via multivariate modeling

(A-24) Modeling of Morphine and RTX in a Porous Media for Intrathecal Drug Delivery

(A-25) Spatial Mutation Mapping In Saudi Arabian Breast Cancer

(A-26) Using an Active-Gel Field Theory to Describe the Formation of Spheroids and Toroids in Collagen

(A-27) Predicting Challenging Behavior in Autism Spectrum Disorder using Nonlinear Classification Techniques

(A-28) Selecting the Most Efficient Method for a Biological Optimization Problem using Deep Bidirectional Encoder Representations from Transformers (BERT)

(A-29) Understanding hormone-controlled tissue remodeling and ovarian follicle rupture using spatiotemporal transcriptomics

(A-30) An Optimized Mobile AI Platform for Remote Cardiovascular Disease Detection and Risk Prediction: ECG-Air V3

(A-31) Computational Modeling of the Role of Ca²⁺ Flux Frequency Decoding by Calmodulin and CaMKII on Actin Polymerization Dynamics and Dendritic Spine Morphology

(A-32) Modeling bivalent avidity of GAB1-PTPN11 binding in SpringSaLaD

(A-33) Model-Dependent Characteristics of Model-Agnostic Variable Importance Analysis in Machine Learning

(A-34) Characterizing Altered Cell States in Blast-Related Traumatic Brain Injuries Using Graph Attention Networks

(A-35) Programmable knockdown of target genes in polycistronic mRNA using de novo-designed sRNA

(A-36) Dopamine Release in the Monkey Striatum and Anticipatory Licking

(A-37) Uncovering chromatin regulator co-dependencies in melanoma through the integration of CRISPR screen and transcriptomics data

(A-38) Spatial Transcriptomic Analysis Regarding Wound Healing in Mouse Skin

(A-39) Comparing Predictive Machine Learning Models’ Capacity to Objectively Predict Dyspnea

(A-40) Systems Biology Modeling of Inflammasomes Impacting Hypertension

(B-41) Python Agent-Based Modeling to Investigate Neural Rosette Formation

(B-42) Visualizing Ovarian Cancer Fate in Response to Chemotherapy

(B-43) Evaluation of Transmembrane Extracellular Ligand Dimerization Actuator (ELDA) Receptors Activated by Stimulatory Ligand Peptides

(B-44) Computational Analysis of Disease Progression in Pediatric Pulmonary Arterial Hypertension

(B-45) The use of Transcriptomics and Microscopy to investigate Volumetric Muscle Loss injuries

(B-46) Phenomena of cell migration in free space under osmotic pressure

(B-47) Analyzing mouse embryonic stem cell H3.2 single-cell combinatorial indexing sequencing dataset

(B-48) Therapeutic exploitation of interactions and asymmetric vulnerabilities in isogenic and coexisting TNBC cancer cell subpopulations

(B-49) Investigating Cancer-Specific Microbiomes: A Comprehensive Analysis of Tumor-Microenvironment Interactions Using Data Mining

(B-50) Application of Cell Vision Transformer Model for the Precise Segmentation and Classification of Mitochondria

(B-51) ParaView-ing Data at NERSC Remotely Using Jupyter Hub

(B-52) Keytruda: The Key to reversing CD8+ T cell exhaustion?

(B-54) Using biological inspired pattern formation systems as information encoding-decoding devices

(B-55) Population dynamics model of ovarian cancer resistance for adaptive therapy strategies

(B-56) Big Data and Machine Learning Approach to Predict Diabetes Risk for Early Intervention

(B-57) Ethical Challenges of Artificial Intelligence in Dentistry

(M-503) An On-Site Machine Learning Assessment Tool Using Heart Rate Variability (HRV) As a Novel Biomarker for Concussion Diagnosis