Low- and high-level information analyses of transcriptome connecting endometrial-decidua-placental origin of preeclampsia subtypes: A preliminary study
CONCLUSIONS: We identified the transcriptome of endometrial maturation in placental dysfunction that distinguished early- and late-onset PE, and indicated chorioamnionitis as a PE competing risk. This study implied a feasibility to develop and validate the pathogenesis models that include pre-pregnancy and competing risks to decide if it is needed to collect prospective data for PE starting from pre-pregnancy including chorioamnionitis information.PMID:38160306 (Source: Pacific Symposium on Biocomputing)
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Herdiantri Sufriyana Yu-Wei Wu Emily Chia-Yu Su Source Type: research
Deconvolution of Nascent Sequencing Data Using Transcriptional Regulatory Elements
We present here the first attempt at solving the supervised deconvolution problem for run-on nascent sequencing data (GRO-seq and PRO-seq), a readout of active transcription. Then, we develop a novel filtering method suited to the mixed set of promoter and enhancer regions provided by nascent sequencing, and apply best-practice standards from the RNA-seq literature, using in-silico mixtures of cells. Using these methods, we find that enhancer RNAs are highly informative features for supervised deconvolution. In most cases, simple deconvolution methods perform better than more complex ones for solving the nascent deconvolut...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Zachary Maas Rutendo Sigauke Robin Dowell Source Type: research
Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer
Pac Symp Biocomput. 2024;29:579-593.ABSTRACTProtein-protein interactions play an essential role in nearly all biological processes, and it has become increasingly clear that in order to better understand the fundamental processes that underlie disease, we must develop a strong understanding of both their context specificity (e.g., tissue-specificity) as well as their dynamic nature (e.g., how they respond to environmental changes). While network-based approaches have found much initial success in the application of protein-protein interactions (PPIs) towards systems-level explorations of biology, they often overlook the fa...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Ruth Dannenfelser Vicky Yao Source Type: research
Lymphocyte Count Derived Polygenic Score and Interindividual Variability in CD4 T-cell Recovery in Response to Antiretroviral Therapy
Pac Symp Biocomput. 2024;29:594-610.ABSTRACTAccess to safe and effective antiretroviral therapy (ART) is a cornerstone in the global response to the HIV pandemic. Among people living with HIV, there is considerable interindividual variability in absolute CD4 T-cell recovery following initiation of virally suppressive ART. The contribution of host genetics to this variability is not well understood. We explored the contribution of a polygenic score which was derived from large, publicly available summary statistics for absolute lymphocyte count from individuals in the general population (PGSlymph) due to a lack of publicly ...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Kathleen M Cardone Scott Dudek Karl Keat Yuki Bradford Zinhle Cindi Eric S Daar Roy Gulick Sharon A Riddler Jeffrey L Lennox Phumla Sinxadi David W Haas Marylyn D Ritchie Source Type: research
Polygenic risk scores for cardiometabolic traits demonstrate importance of ancestry for predictive precision medicine
In this study, we present an in-depth evaluation of PRS based on multi-ancestry GWAS for five cardiometabolic phenotypes in the Penn Medicine BioBank (PMBB) followed by a phenome-wide association study (PheWAS). We examine the PRS performance across all individuals and separately in African ancestry (AFR) and EUR ancestry groups. For AFR individuals, PRS derived using the multi-ancestry LD panel showed a higher effect size for four out of five PRSs (DBP, SBP, T2D, and BMI) than those derived from the AFR LD panel. In contrast, for EUR individuals, the multi-ancestry LD panel PRS demonstrated a higher effect size for two ou...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Rachel L Kember Shefali S Verma Anurag Verma Brenda Xiao Anastasia Lucas Colleen M Kripke Renae Judy Jinbo Chen Scott M Damrauer Daniel J Rader Marylyn D Ritchie Source Type: research
intCC: An efficient weighted integrative consensus clustering of multimodal data
Pac Symp Biocomput. 2024;29:627-640.ABSTRACTHigh throughput profiling of multiomics data provides a valuable resource to better understand the complex human disease such as cancer and to potentially uncover new subtypes. Integrative clustering has emerged as a powerful unsupervised learning framework for subtype discovery. In this paper, we propose an efficient weighted integrative clustering called intCC by combining ensemble method, consensus clustering and kernel learning integrative clustering. We illustrate that intCC can accurately uncover the latent cluster structures via extensive simulation studies and a case stud...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Can Huang Pei Fen Kuan Source Type: research
Large language models (llms) and chatgpt for biomedicine
Pac Symp Biocomput. 2024;29:641-644.ABSTRACTLarge Language Models (LLMs) are a type of artificial intelligence that has been revolutionizing various fields, including biomedicine. They have the capability to process and analyze large amounts of data, understand natural language, and generate new content, making them highly desirable in many biomedical applications and beyond. In this workshop, we aim to introduce the attendees to an in-depth understanding of the rise of LLMs in biomedicine, and how they are being used to drive innovation and improve outcomes in the field, along with associated challenges and pitfalls.PMID:...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Cecilia Arighi Steven Brenner Zhiyong Lu Source Type: research
Practical Approaches to Enhancing Fairness, Social Responsibility and the Inclusion of Diverse Viewpoints in Biomedicine
Pac Symp Biocomput. 2024;29:645-649.ABSTRACTThe following sections are included:Workshop DescriptionLearning ObjectivesPresenter InformationAbout the Workshop OrganizersPresentationsSpeaker Presentations.PMID:38160313 (Source: Pacific Symposium on Biocomputing)
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Daphne O Martschenko Nicole Martinez-Martin Meghan Halley Source Type: research
Risk prediction: Methods, Challenges, and Opportunities
Pac Symp Biocomput. 2024;29:650-653.ABSTRACTThe following sections are included:Introduction to the workshopWorkshop Presenters.PMID:38160314 (Source: Pacific Symposium on Biocomputing)
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Ruowang Li Rui Duan Lifang He Jason H Moore Source Type: research
Statistical analysis of single-cell protein data
Pac Symp Biocomput. 2024;29:654-660.ABSTRACTImmune modulation is considered a hallmark of cancer initiation and progression, with immune cell density being consistently associated with clinical outcomes of individuals with cancer. Multiplex immunofluorescence (mIF) microscopy combined with automated image analysis is a novel and increasingly used technique that allows for the assessment and visualization of the tumor microenvironment (TME). Recently, application of this new technology to tissue microarrays (TMAs) or whole tissue sections from large cancer studies has been used to characterize different cell populations in ...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Brooke L Fridley Simon Vandekar Inna Chervoneva Julia Wrobel Siyuan Ma Source Type: research
Tools for assembling the cell: Towards the era of cell structural bioinformatics
Pac Symp Biocomput. 2024;29:661-665.ABSTRACTCells consist of large components, such as organelles, that recursively factor into smaller systems, such as condensates and protein complexes, forming a dynamic multi-scale structure of the cell. Recent technological innovations have paved the way for systematic interrogation of subcellular structures, yielding unprecedented insights into their roles and interactions. In this workshop, we discuss progress, challenges, and collaboration to marshal various computational approaches toward assembling an integrated structural map of the human cell.PMID:38160316 (Source: Pacific Sympo...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Mengzhou Hu Xikun Zhang Andrew Latham Andrej Ε ali Trey Ideker Emma Lundberg Source Type: research
A Conversational Agent for Early Detection of Neurotoxic Effects of Medications through Automated Intensive Observation
We present a fully automated AI-based system for intensive monitoring of cognitive symptoms of neurotoxicity that frequently appear as a result of immunotherapy of hematologic malignancies. Early manifestations of these symptoms are evident in the patient's speech in the form of mild aphasia and confusion and can be detected and effectively treated prior to onset of more serious and potentially life-threatening impairment. We have developed the Automated Neural Nursing Assistant (ANNA) system designed to conduct a brief cognitive assessment several times per day over the telephone for 5-14 days following infusion of the im...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Serguei Pakhomov Jacob Solinsky Martin Michalowski Veronika Bachanova Source Type: research
Leveraging 3D Echocardiograms to Evaluate AI Model Performance in Predicting Cardiac Function on Out-of-Distribution Data
The objective of this project is to leverage 3D echos to simulate realistic human variation of image acquisition and better understand the OOD performance of a previously validated AI model. In doing so, we develop tools for interpreting 3D echo data and quantifiably recreating common variation in image acquisition between sonographers. We also developed a technique for finding good standard 2D views in 3D echo volumes. We found the performance of the AI model we evaluated to be as expected when the view is good, but variations in acquisition position degraded AI model performance. Performance on far from ideal views was p...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Grant Duffy Kai Christensen David Ouyang Source Type: research
BrainSTEAM: A Practical Pipeline for Connectome-based fMRI Analysis towards Subject Classification
Pac Symp Biocomput. 2024;29:53-64.ABSTRACTFunctional brain networks represent dynamic and complex interactions among anatomical regions of interest (ROIs), providing crucial clinical insights for neural pattern discovery and disorder diagnosis. In recent years, graph neural networks (GNNs) have proven immense success and effectiveness in analyzing structured network data. However, due to the high complexity of data acquisition, resulting in limited training resources of neuroimaging data, GNNs, like all deep learning models, suffer from overfitting. Moreover, their capability to capture useful neural patterns for downstrea...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Alexis Li Yi Yang Hejie Cui Carl Yang Source Type: research
MaTiLDA: An Integrated Machine Learning and Topological Data Analysis Platform for Brain Network Dynamics
Pac Symp Biocomput. 2024;29:65-80.ABSTRACTTopological data analysis (TDA) combined with machine learning (ML) algorithms is a powerful approach for investigating complex brain interaction patterns in neurological disorders such as epilepsy. However, the use of ML algorithms and TDA for analysis of aberrant brain interactions requires substantial domain knowledge in computing as well as pure mathematics. To lower the threshold for clinical and computational neuroscience researchers to effectively use ML algorithms together with TDA to study neurological disorders, we introduce an integrated web platform called MaTiLDA. MaTi...
Source: Pacific Symposium on Biocomputing - December 31, 2023 Category: Bioinformatics Authors: Katrina Prantzalos Dipak Upadhyaya Nassim Shafiabadi Guadalupe Fernandez-BacaVaca Nick Gurski Kenneth Yoshimoto Subhashini Sivagnanam Amitava Majumdar Satya S Sahoo Source Type: research
