Table of Contents

• A Containerization Framework for Bioinformatics Software to Advance Scalability, Portability, and MaintainabilityJustin Z. Tam, Alexandra Chua, Adyn Gallagher, Denice Omene, Danielle Okun, Dominic DiFranzo, Brian Y. Chen. [doi]
• 3D Biological/Biomedical Image Registration with enhanced Feature Extraction and Outlier DetectionSahand Hamzehei, Jun Bai, Gianna Raimondi, Rebecca Tripp, Linnaea Ostroff, Sheida Nabavi. [doi]
• Proteus: Towards a Manageability-focused Home-based Health Monitoring InfrastructureMengjing Liu, Mohammed Elbadry, Yindong Hua, Zongxing Xie, Fan Ye 0003. [doi]
• Automatically measuring dyspigmentation severity of the skin using a convolutional neural networkLéa Gazeau, Hang Nguyen. [doi]
• RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep LearningSarah Coffland, Katie Christensen, Filip Jagodzinski, Brian Hutchinson. [doi]
• Generalized Matching Distance: Tumor Phylogeny Comparison Beyond the Infinite Sites AssumptionQuoc Nguyen, Layla Oesper. [doi]
• Smartphone-based Pupillometry for Diagnosis of Ischemic and Hemorrhagic StrokeAnthony James Maxin, Bernice G. Gulek, Rami Shaibani, Alex Mariakakis, Lynn B. McGrath, Michael Levitt. [doi]
• Leveraging Large Language Models for Automatic Hypotheses Testing over Heterogeneous Biological DatabasesHasan M. Jamil, Stephen A Krawetz, Alexander Gow. [doi]
• Deep-Learning Based Cell Segmentation and Deconvolution in Spatial TranscriptomicsMena Soliman Asaad Kamel, Amrut Sarangi, Cindy Qin, Het Barot, Pavel Senin, Sergio Villordo, Sunaal Mathew, Albert Pla Planas, Ziv Bar-Joseph. [doi]
• Root Causal Inference from Single Cell RNA Sequencing with the Negative BinomialEric V. Strobl. [doi]
• Identification of generalizable gene expression biomarkers associated with drug Respose in cell Lines and patientsNoam Auslander, Abdurrahman Elbasir. [doi]
• Canonical Representation of Biological Networks Using Graph ConvolutionMengzhen Li, Mustafa Coskun, Mehmet Koyutürk. [doi]
• Minimizing Reference Bias: The Impute-First Approach for Personalized Genome AnalysisNaga Sai Kavya Vaddadi, Taher Mun, Benjamin Thomas Langmead. [doi]
• TREEMENT: Interpretable Patient-Trial Matching via Personalized Dynamic Tree-based Memory NetworkBrandon Philip Theodorou, Cao Xiao, Jimeng Sun 0001. [doi]
• PhysioMed: A Semantic Web based Framework for Linking Healthcare Information with Computational Physiology ModelsReza Kalbasi, David P. Nickerson, Koray Atalag. [doi]
• Compound RNN to predict MICs using K-Mer Fingerprints and Antibiotic SMILESCory Kromer-Edwards, Suely Oliveira. [doi]
• Reconstructing Phylogenies Using Branch-Variable Substitution Models and Unaligned Biomolecular Sequences: A Performance Study and New Resampling MethodRei Doko, Kevin Liu. [doi]
• Reference-Free Imputation of Targeted Next-Generation Sequence DatasetsArun Nampally, Joseph Kim, Eric Proffitt, Eugene Palovcak, Alix Lacoste. [doi]
• Predicting Opioid Use Outcomes in Minoritized CommunitiesAbhay Goyal, Nimay Parekh, Lam Yin Cheung, Koustuv Saha, Frederick L. Altice, Robin O'Hanlon, Roger Ho Chun Man, Chunki Fong, Christian Poellabauer, Honoria Guarino, Pedro Mateu-Gelabert, Navin Kumar. [doi]
• Robust Retinal Layer Segmentation Using OCT B-Scans: A Novel Approach Based on Pix2Pix Generative Adversarial NetworkAdarsh Gadari, Sandeep Chandra Bollepalli, Mohammed Nasar Ibrahim, Sahel Jose'-Alian, Jay Chhablani, Shan Suthaharan, Kiran Kumar Vupparaboina. [doi]
• A Sequence-Based Prediction Model of Vesicular Transport Proteins Using Ensemble Deep LearningNguyen-Quoc-Khanh Le, Quang-Hien Kha. [doi]
• AcrTransAct: Pre-trained Protein Transformer Models for the Detection of Type I Anti-CRISPR ActivitiesMoein Hasani, Chantel N. Trost, Nolen Timmerman, Lingling Jin. [doi]
• An Approach to Developing Benchmark Datasets for Protein Secondary Structure Segmentation from Cryo-EM Density MapsThu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He 0002. [doi]
• Benchmarking deep learning models and classical de novo sequencing tools for immunopeptidomicsLiang Xue, Mykola Bordyuh, Djork-Arne Clevert, Robert Stanton. [doi]
• Phylogenetic Placement of Aligned Genomes and Metagenomes with Non-tree-like Evolutionary HistoriesMd Alamin, Kevin J. Liu. [doi]
• Synergistic Fusion of Graph and Transformer Features for Enhanced Molecular Property PredictionMukkamala Venkata Sai Prakash, Siddartha Reddy, Ganesh Parab, Varun V, Vishal Vaddina, Saisubramaniam Gopalakrishnan. [doi]
• CodonBERT: Using BERT for Sentiment Analysis to Better Predict Genes with Low ExpressionAshley Nicole Babjac, Zhixiu Lu, Scott J. Emrich. [doi]
• Interoperable Healthcare with Blockchain: A Data Transfer ModelNiranjan Sahi, Anda Liang, Sean Mchale, Wyn Van Devanter, Peng Zhang. [doi]
• Vulture: VULnerabilities in impuTing drUg REsistanceAysegul Bumin, Megan Shah, Kejun Huang, Tamer Kahveci. [doi]
• Enhancing Cryo-EM Particle Picking Through Consistency Model-based Latent Space DenoiserAlif Bin Abdul Qayyum, Xiaoning Qian, Byung-Jun Yoon. [doi]
• Phase Synchronization in Brain Collective DynamicsGangadhar Katuri, Epaminondas Rosa Jr., Rosangela Follmann. [doi]
• Self-Supervised Learning with Touchscreen Typing. A Generalizable Strategy for Parkinson's Disease Detection Across DatasetsShikha Tripathi, Alejandro Acien, Ashley A Holmes, Teresa Arroyo-Gallego, Luca Giancardo. [doi]
• Retrieval-Augmented Large Language Models for Adolescent Idiopathic Scoliosis Patients in Shared Decision-MakingWenqi Shi, Yuchen Zhuang, Yuanda Zhu, Henry J. Iwinski, J. Michael Wattenbarger, May Dongmei Wang. [doi]
• A Comparative Analysis of Transformer-based Protein Language Models for Remote Homology PredictionAnowarul Kabir, Asher Moldwin, Amarda Shehu. [doi]
• Deep learning-based survival prediction using DNA methylation-derived 3D genomic informationJeewon Yang, DoHoon Lee, Bonil Koo, Dabin Jeong, Sun Kim. [doi]
• Modeling Human Frailty with a Smart Home-Based Approximation of EntropyKatherine A. Wuestney, Beiyu Lin, Diane J. Cook, Roschelle L. Fritz. [doi]
• Beyond Motor Symptoms: Toward a Comprehensive Grading of Parkinson's Disease SeverityMorteza Rahimi, Zeina Al Masry, John Michael Templeton, Sandra L. Schneider, Christian Poellabauer. [doi]
• PINet: Privileged Information Improve the Interpretablity and generalization of structural MRI in Alzheimer's DiseaseZijia Tang, Tonglin Zhang, Qianqian Song, Jing Su, Baijian Yang. [doi]
• RAmbler: de novo genome assembly of complex repetitive regionsSakshar Chakravarty, Glennis Logsdon, Stefano Lonardi. [doi]
• Multi-Group Tensor Canonical Correlation AnalysisZhuoping Zhou, Boning Tong, Davoud Ataee Tarzanagh, Bojian Hou, Andrew J. Saykin, Qi Long, Li Shen 0001. [doi]
• Predicting Drug-drug Interactions Using Heterogeneous Graph Attention NetworksFarhan Tanvir, Khaled Mohammed Saifuddin, Muhammad Ifte Khairul Islam, Esra Akbas. [doi]
• CORE: Comparable, Open, Reliable, Extensible Software: An Experience Report of Four Flux Balance Analysis ToolsAlexis L. Marsh, Myra B. Cohen, Robert W. Cottingham. [doi]
• Breast-Density Semantic Segmentation with Probability Scaling for BI-RADS Assessment using DeepLabV3Conrad T. Testagrose, Vikash Gupta, Barbaros S. Erdal, Richard D. White, Robert W. Maxwell, Xudong Liu, Indika Kahanda, Sherif Elfayoumy, William Klostermeyer, Mutlu Demirer. [doi]
• Understanding the Evolutionary Conservation of the Ilp1 gene across Drosophila: Genomics Education PartnershipElias A Ciudad, Lori Boies, Muskaan Tayal. [doi]
• Investigation of Drug Repurposing Opportunities Using Side-effects data, Topic Modelling and Clustering AlgorithmsPritish Ranjan, Shyam Sundar Das, Narayanan Ramamurthi. [doi]
• Model Confidence Calibration for Reliable COVID-19 Early Screening via Audio Signal AnalysisMicky C. Nnamdi, Ben Junior Tamo, Sara Stackpole, Wenqi Shi, Benoit Marteau, May Dongmei Wang. [doi]
• Enabling the Informed Patient Paradigm with Secure and Personalized Medical Question AnsweringJoel Oduro-Afriyie, Hasan M. Jamil. [doi]
• Genetic Site-Aware Three-Dimensional Layout Algorithm for Variation GraphsDeepro Pasha, Yohei Rosen, Maxim Kuznetsov, Benedict Paten. [doi]
• Exploring Pair-Aware Triangular Attention for Biomedical Relation ExtractionLei Chen, Junhao Su, Tak Wah Lam, Ruibang Luo. [doi]
• Localized, Non-parametric Detection of RNA Structural Modification using Nanopore BasecallingJ. White Bear, Grégoire De Bisschop, Eric Lécuyer, Jérôme Waldispühl. [doi]
• A Comparison of Machine Learning Models with Data Augmentation Techniques for Skeleton-based Human Action RecognitionChu Xin, Seokhwan Kim, Kyoung Shin Park. [doi]
• Identifying Impactful Pairs of Insertion Mutations in ProteinsChangrui Li, Filip Jagodzinski. [doi]
• Concise Ranked Functional Enrichment AnalysisXinglin Jia, An Phan, Claus Kadelka. [doi]
• Using Large Language Models to Translate Machine Results to Human ResultsJonathan W. Stubblefield, Trishna Niraula. [doi]
• Nucleotide String Indexing using Range MatchingAlon Rashelbach, Ori Rottenstreich, Mark Silberstein. [doi]
• Doxorubicin Efficacy Prediction for Glioblastomas Using Deep Learning and Differnetial EquationsArnav Garg, Pranav Narala, Maruthi Vemula. [doi]
• Phylogenomics using Compression Distances: Incorporating Rate Heterogeneity and Amino Acid PropertiesEdward L. Braun. [doi]
• A Multi-Layered GRU Model for COVID-19 Patient Representation and Phenotyping from Large-Scale EHR DataArpita Saha, Maggie Samaan, Bo Peng, Xia Ning. [doi]
• Adolescent Idiopathic Scoliosis Patient Subphenotyping for Surgical Planning and Improved Patient OutcomesBen Junior Tamo, Wenqi Shi, Yuanda Zhu, Micky C. Nnamdi, Henry J. Iwinski, J. Michael Wattenbarger, May Dongmei Wang. [doi]
• Computational Methods to Determine Genetic Factors in Nicotine DependencyKevin Kaizhe Yang, Julian Stanley. [doi]
• The Impact of Species Tree Estimation Error on Cophylogenetic ReconstructionJulia Zheng, Yuya Nishida, Alicja Okrasinska, Gregory M. Bonito, Elizabeth A. C. Heath-Heckman, Kevin J. Liu. [doi]
• Deconvolution of cell-free DNA in cancer liquid biopsy using a deep AutoEncoderFelix Jackson, Thomas Lukasiewicz. [doi]
• CBOEP: Generating negative enhancer-promoter interactions to train classifiersTsukasa Koga, Osamu Maruyama. [doi]
• Quantifying Recombination Bias in Viral Evolution Using Persistent HomologySavik Kinger. [doi]
• Optimizing K-Mer Fingerprint Generation for Machine LearningCory Kromer-Edwards. [doi]
• GRAPPEL: A Graph-based Approach for Early Risk Assessment of Acute Hypertension in Critical CareSonal Jha, Wu-chun Feng. [doi]
• An Ensemble Machine Learning Approach for Benchmarking and Selection of scRNA-seq Integration MethodsKonghao Zhao, Sapan Bhandari, Nathan P. Whitener, Jason M. Grayson, Natalia Khuri. [doi]
• Text-to-ESQ: A Two-Stage Controllable Approach for Efficient Retrieval of Vaccine Adverse Events from NoSQL DatabaseWenlong Zhang, Kangping Zeng, Xinming Yang, Tian Shi, Ping Wang 0024. [doi]
• ProMVR-Interactive Protein Educational ToolTianshu Xu, Venkata VB Yallapragada, Mark Tangney, Sabin Tabirca. [doi]
• On de novo Bridging Paired-end RNA-seq DataXiang Li, Mingfu Shao. [doi]
• AlphaFold2 Model Refinement Using Structure DecoysMaytha Alshammari, Jing He 0002, Willy Wriggers. [doi]
• Real-Time Monitoring of Health Security Attacks with R-based Data Visualization DashboardMridula Shan. [doi]
• k-mers with the Edit DistanceLeran Ma, Ke Chen 0011, Mingfu Shao. [doi]
• Structure- and Energy-based Analysis of Small Molecule Ligand Binding to Steroid Nuclear ReceptorsMegan Herceg, Amarda Shehu. [doi]
• Identification of therapeutic targets for muscle atrophy via analyzing transcriptomic profiles with systems biology approachesAhyoung Choi, No Soo Kim, Aeyung Kim, Haeseung Lee, Hyunjin Shin. [doi]
• Formulating a method to analyse the differential expression of co-occurrence networks for small-sampled microbiome dataNandini Amit Gadhia, Michalis Smyrnakis, Po-Yu Liu, Damer Blake, Melanie Hay, Anh Nguyen, Dong Xia, Ritesh Krishna, Dominic Richards. [doi]
• AutoML in Drug Discovery: Side-Effects Prediction Using AutoGluon Framework and Its Applications in Drug DiscoveryAyush Garg, Shyam Sundar Das, Narayanan Ramamurthi. [doi]
• Drug Target Prioritization Based on Ligand Binding Pocket and Disease-Target Association ScoresAyush Garg, Shyam Sundar Das, Narayanan Ramamurthi. [doi]
• Numerically stable algorithm for Inverse Kinematics of 6R problem and its applications to macrocyclesXin Cao, Mikhail Ignatov, George Jones, Sara N. Pollock, Evangelos A. Coutsias, Dima Kozakov. [doi]
• FinFax: Fast Interpretation of Fax with NLPOmer Anjum, Luyao Chen, Ryan Denlinger, Ejaz Anam, Dongsheng Yuan, Connie Wooldridge, Martin J. Citardi, Jiajie Zhang, Hua Xu 0001, Xiaoqian Jiang. [doi]
• Choice Over Effort: Mapping and Diagnosing Augmented Whole Slide Image Datasets with Training DynamicsWenqi Shi, Benoit Louis Marteau, Felipe O. Giuste, May Dongmei Wang. [doi]
• Deciphering the contribution of 3D interactions between cis-regulatory elements and promoters to regulate gene expression using graph neural networksYang Chen, Elissa Lei. [doi]
• Assessing Fairness of AlphaFold2 Prediction of Protein 3D StructuresUsman L. Abbas, Jin Chen, Qing Shao. [doi]
• Gene Regulatory Network Based Toxicity Classification and Prediction: A DILI Case StudyShreyas U. Hirway, Xiang Yao, Fetene Tekle, Thomas De Marchin, Onyi Irrechukwu, Freddy Van Goethem. [doi]
• Contrastive Learning in Single-cell Multiomics ClusteringBingjun Li, Sheida Nabavi. [doi]
• SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogensAdvait Balaji, Yunxi Liu, Michael G. Nute, Bingbing Hu, Anthony D. Kappell, Danielle S. Lesassier, Gene D. Godbold, Krista Ternus, Todd J. Treangen. [doi]
• MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasksRui Li, Andrew Wen, Jing Gao 0004, Hongfang Liu. [doi]
• Clinical Trial Active LearningZoe Fowler, Kiran Premdat Kokilepersaud, Mohit Prabhushankar, Ghassan Alregib. [doi]
• A Distributed Alignment-free Pipeline for Human SNPs GenotypingLorenzo Di Rocco, Umberto Ferraro Petrillo. [doi]
• Multimodality-aware Intra-dialytic Hypotension Classifier: A Bilingual NLP Approach to Classify Dialysis RecordsJu-Yeh Yang, Tsung-Chun Lee, Chih-Yu Jian, Chih-Chung Hsu. [doi]
• Designing Helicobacter pylori as an Anticancer Bacterial VectorSelina Zhang, Jake Yue Chen. [doi]
• Large-scale Dataset and Effective Model for Variant-Disease Associations ExtractionLei Chen, Junhao Su, Zhenxian Zheng, Tak Wah Lam, Ruibang Luo. [doi]
• Augmenting nutritional metabolomics with a genome-scale metabolic model for assessment of diet intakeKowshika Sarker, Ruoqing Zhu, Hannah D. Holscher, ChengXiang Zhai. [doi]
• Evaluating Drug Effectiveness for Antihypertensives in Heart Failure Prognosis: Leveraging Composite Clinical Endpoints and Biomarkers from Electronic Health RecordsShaika Chowdhury, Yongbin Chen, Xiao Ma, Qiying Dai, Yue Yu, Nansu Zong. [doi]
• Automated Focus Restoration for High-throughput Phase Contrast Time-lapse Microscopy with De-noising Diffusion Probabilistic ModelKwan-Ling Wu, Melisa Montalvo, Prashant Menon, Badrinath Roysam, Navin Varadarajan. [doi]
• Continuous Stress Monitoring for Healthcare Workers: Evaluating Generalizability Across Real-World DatasetsJordan Li Cahoon, Luis Antonio Garcia. [doi]
• Predicting Tumor Mutational Burden and Survival in Head and Neck Squamous Cancer Patients Using Machine Learning and Bioinformatics ApproachesNguyen-Kieu Viet-Nhi, Nguyen-Quoc-Khanh Le, Vu Cong Truc, Thi Thuy Nguyen, Tran Nguyen Anh Duy, Nguyen Tu Thai Bao, How Tseng, Shih-Han Hung. [doi]
• Performance Evaluation of Semantic Segmentation Models with and without Attention for White Blood Cells SegmentationRajshree Jodha, Priyanka Mishra, J. Angel Arul Jothi, Sameer Saifi, Abhishek Purohit. [doi]
• An Integrative Approach to Building Regulatory Potential-Weighted Gene Regulatory Networks: A Leiomyoma Case StudyBrandon Edward Lukas, Yang Dai. [doi]
• SPOT: Sequential Predictive Modeling of Clinical Trial Outcome with Meta-LearningZifeng Wang 0010, Cao Xiao, Jimeng Sun 0001. [doi]
• Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and SequenceFelix Quintana, Todd J. Treangen, Lydia E. Kavraki. [doi]
• Dual ICA to extract interacting sets of genes and conditions from transcriptomic dataSanjeevani Choudhery, Thomas R. Ioerger. [doi]
• Sectioning biomedical abstracts using pointer networksMehmet Efruz Karabulut, K. Vijay-Shanker. [doi]
• Capturing Solvent-System Effects in B-Cell Epitope Prediction with the HAPTIC3/HEPTAD2 User Toolkit (HUT2)Salvador Eugenio C. Caoili. [doi]
• A Model of Cell Population Dynamics in Skeletal Muscle RegenerationRenad Al-Ghazawi, Theodore J. Perkins, Xiaojian Shao. [doi]
• Temperature Effects on Neuronal SynchronizationTwinkle Jaswal, Epaminondas Rosa Jr., Rosangela Follmann. [doi]
• Can Attention Be Used to Explain EHR-Based Mortality Prediction Tasks: A Case Study on Hemorrhagic StrokeQizhang Feng, Jiayi Yuan, Forhan Bin Emdad, Karim Hanna, Xia Hu, Zhe He 0001. [doi]
• Physics-Guided Deep Generative Model For New Ligand DiscoveryDikshant Sagar, Ali Risheh, Nida Sheikh, Negin Forouzesh. 1-9 [doi]