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Viewing Publication 1 - 100 from 1719

2023

SPOT: Sequential Predictive Modeling of Clinical Trial Outcome with Meta-LearningZifeng Wang 0010, Cao Xiao, Jimeng Sun 0001. bcb 2023: [doi]

Assessing Fairness of AlphaFold2 Prediction of Protein 3D StructuresUsman L. Abbas, Jin Chen, Qing Shao. bcb 2023: [doi]

A Model of Cell Population Dynamics in Skeletal Muscle RegenerationRenad Al-Ghazawi, Theodore J. Perkins, Xiaojian Shao. bcb 2023: [doi]

Phylogenetic Placement of Aligned Genomes and Metagenomes with Non-tree-like Evolutionary HistoriesMd Alamin, Kevin J. Liu. bcb 2023: [doi]

AlphaFold2 Model Refinement Using Structure DecoysMaytha Alshammari, Jing He 0002, Willy Wriggers. bcb 2023: [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. bcb 2023: [doi]

Identification of generalizable gene expression biomarkers associated with drug Respose in cell Lines and patientsNoam Auslander, Abdurrahman Elbasir. bcb 2023: [doi]

CodonBERT: Using BERT for Sentiment Analysis to Better Predict Genes with Low ExpressionAshley Nicole Babjac, Zhixiu Lu, Scott J. Emrich. bcb 2023: [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. bcb 2023: [doi]

Localized, Non-parametric Detection of RNA Structural Modification using Nanopore BasecallingJ. White Bear, Grégoire De Bisschop, Eric Lécuyer, Jérôme Waldispühl. bcb 2023: [doi]

Phylogenomics using Compression Distances: Incorporating Rate Heterogeneity and Amino Acid PropertiesEdward L. Braun. bcb 2023: [doi]

Vulture: VULnerabilities in impuTing drUg REsistanceAysegul Bumin, Megan Shah, Kejun Huang, Tamer Kahveci. bcb 2023: [doi]

Continuous Stress Monitoring for Healthcare Workers: Evaluating Generalizability Across Real-World DatasetsJordan Li Cahoon, Luis Antonio Garcia. bcb 2023: [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. bcb 2023: [doi]

Capturing Solvent-System Effects in B-Cell Epitope Prediction with the HAPTIC3/HEPTAD2 User Toolkit (HUT2)Salvador Eugenio C. Caoili. bcb 2023: [doi]

RAmbler: de novo genome assembly of complex repetitive regionsSakshar Chakravarty, Glennis Logsdon, Stefano Lonardi. bcb 2023: [doi]

Large-scale Dataset and Effective Model for Variant-Disease Associations ExtractionLei Chen, Junhao Su, Zhenxian Zheng, Tak Wah Lam, Ruibang Luo. bcb 2023: [doi]

Exploring Pair-Aware Triangular Attention for Biomedical Relation ExtractionLei Chen, Junhao Su, Tak Wah Lam, Ruibang Luo. bcb 2023: [doi]

Deciphering the contribution of 3D interactions between cis-regulatory elements and promoters to regulate gene expression using graph neural networksYang Chen, Elissa Lei. bcb 2023: [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. bcb 2023: [doi]

Dual ICA to extract interacting sets of genes and conditions from transcriptomic dataSanjeevani Choudhery, Thomas R. Ioerger. bcb 2023: [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. bcb 2023: [doi]

Understanding the Evolutionary Conservation of the Ilp1 gene across Drosophila: Genomics Education PartnershipElias A Ciudad, Lori Boies, Muskaan Tayal. bcb 2023: [doi]

RoseNet: Predicting Energy Metrics of Double InDel Mutants Using Deep LearningSarah Coffland, Katie Christensen, Filip Jagodzinski, Brian Hutchinson. bcb 2023: [doi]

Reconstructing Phylogenies Using Branch-Variable Substitution Models and Unaligned Biomolecular Sequences: A Performance Study and New Resampling MethodRei Doko, Kevin Liu. bcb 2023: [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. bcb 2023: [doi]

Clinical Trial Active LearningZoe Fowler, Kiran Premdat Kokilepersaud, Mohit Prabhushankar, Ghassan Alregib. bcb 2023: [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. bcb 2023: [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. bcb 2023: [doi]

Doxorubicin Efficacy Prediction for Glioblastomas Using Deep Learning and Differnetial EquationsArnav Garg, Pranav Narala, Maruthi Vemula. bcb 2023: [doi]

AutoML in Drug Discovery: Side-Effects Prediction Using AutoGluon Framework and Its Applications in Drug DiscoveryAyush Garg, Shyam Sundar Das, Narayanan Ramamurthi. bcb 2023: [doi]

Drug Target Prioritization Based on Ligand Binding Pocket and Disease-Target Association ScoresAyush Garg, Shyam Sundar Das, Narayanan Ramamurthi. bcb 2023: [doi]

Automatically measuring dyspigmentation severity of the skin using a convolutional neural networkLéa Gazeau, Hang Nguyen. bcb 2023: [doi]

3D Biological/Biomedical Image Registration with enhanced Feature Extraction and Outlier DetectionSahand Hamzehei, Jun Bai, Gianna Raimondi, Rebecca Tripp, Linnaea Ostroff, Sheida Nabavi. bcb 2023: [doi]

Structure- and Energy-based Analysis of Small Molecule Ligand Binding to Steroid Nuclear ReceptorsMegan Herceg, Amarda Shehu. bcb 2023: [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. bcb 2023: [doi]

Deconvolution of cell-free DNA in cancer liquid biopsy using a deep AutoEncoderFelix Jackson, Thomas Lukasiewicz. bcb 2023: [doi]

Leveraging Large Language Models for Automatic Hypotheses Testing over Heterogeneous Biological DatabasesHasan M. Jamil, Stephen A Krawetz, Alexander Gow. bcb 2023: [doi]

Temperature Effects on Neuronal SynchronizationTwinkle Jaswal, Epaminondas Rosa Jr., Rosangela Follmann. bcb 2023: [doi]

GRAPPEL: A Graph-based Approach for Early Risk Assessment of Acute Hypertension in Critical CareSonal Jha, Wu-chun Feng. bcb 2023: [doi]

Concise Ranked Functional Enrichment AnalysisXinglin Jia, An Phan, Claus Kadelka. bcb 2023: [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. bcb 2023: [doi]

A Comparative Analysis of Transformer-based Protein Language Models for Remote Homology PredictionAnowarul Kabir, Asher Moldwin, Amarda Shehu. bcb 2023: [doi]

PhysioMed: A Semantic Web based Framework for Linking Healthcare Information with Computational Physiology ModelsReza Kalbasi, David P. Nickerson, Koray Atalag. bcb 2023: [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. bcb 2023: [doi]

Sectioning biomedical abstracts using pointer networksMehmet Efruz Karabulut, K. Vijay-Shanker. bcb 2023: [doi]

Phase Synchronization in Brain Collective DynamicsGangadhar Katuri, Epaminondas Rosa Jr., Rosangela Follmann. bcb 2023: [doi]

Quantifying Recombination Bias in Viral Evolution Using Persistent HomologySavik Kinger. bcb 2023: [doi]

CBOEP: Generating negative enhancer-promoter interactions to train classifiersTsukasa Koga, Osamu Maruyama. bcb 2023: [doi]

Optimizing K-Mer Fingerprint Generation for Machine LearningCory Kromer-Edwards. bcb 2023: [doi]

Compound RNN to predict MICs using K-Mer Fingerprints and Antibiotic SMILESCory Kromer-Edwards, Suely Oliveira. bcb 2023: [doi]

A Sequence-Based Prediction Model of Vesicular Transport Proteins Using Ensemble Deep LearningNguyen-Quoc-Khanh Le, Quang-Hien Kha. bcb 2023: [doi]

Identifying Impactful Pairs of Insertion Mutations in ProteinsChangrui Li, Filip Jagodzinski. bcb 2023: [doi]

Contrastive Learning in Single-cell Multiomics ClusteringBingjun Li, Sheida Nabavi. bcb 2023: [doi]

Canonical Representation of Biological Networks Using Graph ConvolutionMengzhen Li, Mustafa Coskun, Mehmet Koyutürk. bcb 2023: [doi]

MLGAN: a Meta-Learning based Generative Adversarial Network adapter for rare disease differentiation tasksRui Li, Andrew Wen, Jing Gao 0004, Hongfang Liu. bcb 2023: [doi]

Proteus: Towards a Manageability-focused Home-based Health Monitoring InfrastructureMengjing Liu, Mohammed Elbadry, Yindong Hua, Zongxing Xie, Fan Ye 0003. bcb 2023: [doi]

An Integrative Approach to Building Regulatory Potential-Weighted Gene Regulatory Networks: A Leiomyoma Case StudyBrandon Edward Lukas, Yang Dai. bcb 2023: [doi]

k-mers with the Edit DistanceLeran Ma, Ke Chen 0011, Mingfu Shao. bcb 2023: [doi]

CORE: Comparable, Open, Reliable, Extensible Software: An Experience Report of Four Flux Balance Analysis ToolsAlexis L. Marsh, Myra B. Cohen, Robert W. Cottingham. bcb 2023: [doi]

Reference-Free Imputation of Targeted Next-Generation Sequence DatasetsArun Nampally, Joseph Kim, Eric Proffitt, Eugene Palovcak, Alix Lacoste. bcb 2023: [doi]

Generalized Matching Distance: Tumor Phylogeny Comparison Beyond the Infinite Sites AssumptionQuoc Nguyen, Layla Oesper. bcb 2023: [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. bcb 2023: [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. bcb 2023: [doi]

Enabling the Informed Patient Paradigm with Secure and Personalized Medical Question AnsweringJoel Oduro-Afriyie, Hasan M. Jamil. bcb 2023: [doi]

Genetic Site-Aware Three-Dimensional Layout Algorithm for Variation GraphsDeepro Pasha, Yohei Rosen, Maxim Kuznetsov, Benedict Paten. bcb 2023: [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. bcb 2023: [doi]

Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and SequenceFelix Quintana, Todd J. Treangen, Lydia E. Kavraki. bcb 2023: [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. bcb 2023: [doi]

Investigation of Drug Repurposing Opportunities Using Side-effects data, Topic Modelling and Clustering AlgorithmsPritish Ranjan, Shyam Sundar Das, Narayanan Ramamurthi. bcb 2023: [doi]

Nucleotide String Indexing using Range MatchingAlon Rashelbach, Ori Rottenstreich, Mark Silberstein. bcb 2023: [doi]

A Distributed Alignment-free Pipeline for Human SNPs GenotypingLorenzo Di Rocco, Umberto Ferraro Petrillo. bcb 2023: [doi]

Physics-Guided Deep Generative Model For New Ligand DiscoveryDikshant Sagar, Ali Risheh, Nida Sheikh, Negin Forouzesh. bcb 2023: 1-9 [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. bcb 2023: [doi]

Interoperable Healthcare with Blockchain: A Data Transfer ModelNiranjan Sahi, Anda Liang, Sean Mchale, Wyn Van Devanter, Peng Zhang. bcb 2023: [doi]

Augmenting nutritional metabolomics with a genome-scale metabolic model for assessment of diet intakeKowshika Sarker, Ruoqing Zhu, Hannah D. Holscher, ChengXiang Zhai. bcb 2023: [doi]

Real-Time Monitoring of Health Security Attacks with R-based Data Visualization DashboardMridula Shan. bcb 2023: [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. bcb 2023: [doi]

Root Causal Inference from Single Cell RNA Sequencing with the Negative BinomialEric V. Strobl. bcb 2023: [doi]

Using Large Language Models to Translate Machine Results to Human ResultsJonathan W. Stubblefield, Trishna Niraula. bcb 2023: [doi]

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. bcb 2023: [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. bcb 2023: [doi]

Predicting Drug-drug Interactions Using Heterogeneous Graph Attention NetworksFarhan Tanvir, Khaled Mohammed Saifuddin, Muhammad Ifte Khairul Islam, Esra Akbas. bcb 2023: [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. bcb 2023: [doi]

TREEMENT: Interpretable Patient-Trial Matching via Personalized Dynamic Tree-based Memory NetworkBrandon Philip Theodorou, Cao Xiao, Jimeng Sun 0001. bcb 2023: [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. bcb 2023: [doi]

Minimizing Reference Bias: The Impute-First Approach for Personalized Genome AnalysisNaga Sai Kavya Vaddadi, Taher Mun, Benjamin Thomas Langmead. bcb 2023: [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. bcb 2023: [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. bcb 2023: [doi]

Modeling Human Frailty with a Smart Home-Based Approximation of EntropyKatherine A. Wuestney, Beiyu Lin, Diane J. Cook, Roschelle L. Fritz. bcb 2023: [doi]

A Comparison of Machine Learning Models with Data Augmentation Techniques for Skeleton-based Human Action RecognitionChu Xin, Seokhwan Kim, Kyoung Shin Park. bcb 2023: [doi]

ProMVR-Interactive Protein Educational ToolTianshu Xu, Venkata VB Yallapragada, Mark Tangney, Sabin Tabirca. bcb 2023: [doi]

Benchmarking deep learning models and classical de novo sequencing tools for immunopeptidomicsLiang Xue, Mykola Bordyuh, Djork-Arne Clevert, Robert Stanton. bcb 2023: [doi]

Computational Methods to Determine Genetic Factors in Nicotine DependencyKevin Kaizhe Yang, Julian Stanley. bcb 2023: [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. bcb 2023: [doi]

Deep learning-based survival prediction using DNA methylation-derived 3D genomic informationJeewon Yang, DoHoon Lee, Bonil Koo, Dabin Jeong, Sun Kim. bcb 2023: [doi]

Designing Helicobacter pylori as an Anticancer Bacterial VectorSelina Zhang, Jake Yue Chen. bcb 2023: [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. bcb 2023: [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. bcb 2023: [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. bcb 2023: [doi]

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2023

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