BCB

Publications

2023

Abhay 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
Predicting Opioid Use Outcomes in Minoritized Communities. BCB (2023)
Ben Junior Tamo, Wenqi Shi, Yuanda Zhu, Micky C. Nnamdi, Henry J. Iwinski, J. Michael Wattenbarger, May Dongmei Wang
Adolescent Idiopathic Scoliosis Patient Subphenotyping for Surgical Planning and Improved Patient Outcomes. BCB (2023)
Sahand Hamzehei, Jun Bai, Gianna Raimondi, Rebecca Tripp, Linnaea Ostroff, Sheida Nabavi
3D Biological/Biomedical Image Registration with enhanced Feature Extraction and Outlier Detection. BCB (2023)
Hasan M. Jamil, Stephen A Krawetz, Alexander Gow
Leveraging Large Language Models for Automatic Hypotheses Testing over Heterogeneous Biological Databases. BCB (2023)
Gangadhar Katuri, Epaminondas Rosa Jr., Rosangela Follmann
Phase Synchronization in Brain Collective Dynamics. BCB (2023)
Md Alamin, Kevin J. Liu
Phylogenetic Placement of Aligned Genomes and Metagenomes with Non-tree-like Evolutionary Histories. BCB (2023)
Arnav Garg, Pranav Narala, Maruthi Vemula
Doxorubicin Efficacy Prediction for Glioblastomas Using Deep Learning and Differnetial Equations. BCB (2023)
Qizhang Feng, Jiayi Yuan, Forhan Bin Emdad, Karim Hanna, Xia Hu, Zhe He
Can Attention Be Used to Explain EHR-Based Mortality Prediction Tasks: A Case Study on Hemorrhagic Stroke. BCB (2023)
Shreyas U. Hirway, Xiang Yao, Fetene Tekle, Thomas De Marchin, Onyi Irrechukwu, Freddy Van Goethem
Gene Regulatory Network Based Toxicity Classification and Prediction: A DILI Case Study. BCB (2023)
Dikshant Sagar, Ali Risheh, Nida Sheikh, Negin Forouzesh
Physics-Guided Deep Generative Model For New Ligand Discovery. BCB (2023)
Tianshu Xu, Venkata VB Yallapragada, Mark Tangney, Sabin Tabirca
ProMVR-Interactive Protein Educational Tool. BCB (2023)
Yang Chen, Elissa P. Lei
Deciphering the contribution of 3D interactions between cis-regulatory elements and promoters to regulate gene expression using graph neural networks. BCB (2023)
Omer Anjum, Luyao Chen, Ryan Denlinger, Ejaz Anam, Dongsheng Yuan, Connie Wooldridge, Martin J. Citardi, Jiajie Zhang, Hua Xu, Xiaoqian Jiang
FinFax: Fast Interpretation of Fax with NLP. BCB (2023)
Mukkamala Venkata Sai Prakash, Siddartha Reddy, Ganesh Parab, Varun V, Vishal Vaddina, Saisubramaniam Gopalakrishnan
Synergistic Fusion of Graph and Transformer Features for Enhanced Molecular Property Prediction. BCB (2023)
Justin Z. Tam, Alexandra Chua, Adyn Gallagher, Denice Omene, Danielle Okun, Dominic DiFranzo, Brian Y. Chen
A Containerization Framework for Bioinformatics Software to Advance Scalability, Portability, and Maintainability. BCB (2023)
Mehmet Efruz Karabulut, K. Vijay-Shanker
Sectioning biomedical abstracts using pointer networks. BCB (2023)
Ahyoung Choi, No Soo Kim, Aeyung Kim, Haeseung Lee, Hyunjin Shin
Identification of therapeutic targets for muscle atrophy via analyzing transcriptomic profiles with systems biology approaches. BCB (2023)
Mena Soliman Asaad Kamel, Amrut Sarangi, Cindy Qin, Het Barot, Pavel Senin, Sergio Villordo, Sunaal Mathew, Albert Pla Planas, Ziv Bar-Joseph
Deep-Learning Based Cell Segmentation and Deconvolution in Spatial Transcriptomics. BCB (2023)
Adarsh Gadari, Sandeep Chandra Bollepalli, Mohammed Nasar Ibrahim, Sahel Jose'-Alian, Jay Chhablani, Shan Suthaharan, Kiran Kumar Vupparaboina
Robust Retinal Layer Segmentation Using OCT B-Scans: A Novel Approach Based on Pix2Pix Generative Adversarial Network. BCB (2023)
Ayush Garg, Shyam Sundar Das, Narayanan Ramamurthi
AutoML in Drug Discovery: Side-Effects Prediction Using AutoGluon Framework and Its Applications in Drug Discovery. BCB (2023)
Salvador Eugenio C. Caoili
Capturing Solvent-System Effects in B-Cell Epitope Prediction with the HAPTIC3/HEPTAD2 User Toolkit (HUT2). BCB (2023)
Usman L. Abbas, Jin Chen, Qing Shao
Assessing Fairness of AlphaFold2 Prediction of Protein 3D Structures. BCB (2023)
Alexis L. Marsh, Myra B. Cohen, Robert W. Cottingham
CORE: Comparable, Open, Reliable, Extensible Software: An Experience Report of Four Flux Balance Analysis Tools. BCB (2023)
Quoc Nguyen, Layla Oesper
Generalized Matching Distance: Tumor Phylogeny Comparison Beyond the Infinite Sites Assumption. BCB (2023)
Pritish Ranjan, Shyam Sundar Das, Narayanan Ramamurthi
Investigation of Drug Repurposing Opportunities Using Side-effects data, Topic Modelling and Clustering Algorithms. BCB (2023)
Bingjun Li, Sheida Nabavi
Contrastive Learning in Single-cell Multiomics Clustering. BCB (2023)
Xiang Li, Mingfu Shao
On de novo Bridging Paired-end RNA-seq Data. BCB (2023)
Chu Xin, Seokhwan Kim, Kyoung Shin Park
A Comparison of Machine Learning Models with Data Augmentation Techniques for Skeleton-based Human Action Recognition. BCB (2023)
Konghao Zhao, Sapan Bhandari, Nathan P. Whitener, Jason M. Grayson, Natalia Khuri
An Ensemble Machine Learning Approach for Benchmarking and Selection of scRNA-seq Integration Methods. BCB (2023)
Zhuoping Zhou, Boning Tong, Davoud Ataee Tarzanagh, Bojian Hou, Andrew J. Saykin, Qi Long, Li Shen
Multi-Group Tensor Canonical Correlation Analysis. BCB (2023)
Mridula Shan
Real-Time Monitoring of Health Security Attacks with R-based Data Visualization Dashboard. BCB (2023)
Farhan Tanvir, Khaled Mohammed Saifuddin, Muhammad Ifte Khairul Islam, Esra Akbas
Predicting Drug-drug Interactions Using Heterogeneous Graph Attention Networks. BCB (2023)
Conrad T. Testagrose, Vikash Gupta, Barbaros S. Erdal, Richard D. White, Robert W. Maxwell, Xudong Liu, Indika Kahanda, Sherif Elfayoumy, William Klostermeyer, Mutlu Demirer
Breast-Density Semantic Segmentation with Probability Scaling for BI-RADS Assessment using DeepLabV3. BCB (2023)
Xin Cao, Mikhail Ignatov, George Jones, Sara N. Pollock, Evangelos A. Coutsias, Dima Kozakov
Numerically stable algorithm for Inverse Kinematics of 6R problem and its applications to macrocycles. BCB (2023)
Elias A Ciudad, Lori Boies, Muskaan Tayal
Understanding the Evolutionary Conservation of the Ilp1 gene across Drosophila: Genomics Education Partnership. BCB (2023)
Xinglin Jia, An Phan, Claus Kadelka
Concise Ranked Functional Enrichment Analysis. BCB (2023)
J. White Bear, Grégoire De Bisschop, Eric Lécuyer, Jérôme Waldispühl
Localized, Non-parametric Detection of RNA Structural Modification using Nanopore Basecalling. BCB (2023)
Zifeng Wang, Cao Xiao, Jimeng Sun
SPOT: Sequential Predictive Modeling of Clinical Trial Outcome with Meta-Learning. BCB (2023)
Brandon Philip Theodorou, Cao Xiao, Jimeng Sun
TREEMENT: Interpretable Patient-Trial Matching via Personalized Dynamic Tree-based Memory Network. BCB (2023)
Morteza Rahimi, Zeina Al Masry, John Michael Templeton, Sandra L. Schneider, Christian Poellabauer
Beyond Motor Symptoms: Toward a Comprehensive Grading of Parkinson's Disease Severity. BCB (2023)
Felix Jackson, Thomas Lukasiewicz
Deconvolution of cell-free DNA in cancer liquid biopsy using a deep AutoEncoder. BCB (2023)
Rajshree Jodha, Priyanka Mishra, J. Angel Arul Jothi, Sameer Saifi, Abhishek Purohit
Performance Evaluation of Semantic Segmentation Models with and without Attention for White Blood Cells Segmentation. BCB (2023)
Anthony James Maxin, Bernice G. Gulek, Rami Shaibani, Alex Mariakakis, Lynn B. McGrath, Michael Levitt
Smartphone-based Pupillometry for Diagnosis of Ischemic and Hemorrhagic Stroke. BCB (2023)
Noam Auslander, Abdurrahman Elbasir
Identification of generalizable gene expression biomarkers associated with drug Respose in cell Lines and patients. BCB (2023)
Shaika Chowdhury, Yongbin Chen, Xiao Ma, Qiying Dai, Yue Yu, Nansu Zong
Evaluating Drug Effectiveness for Antihypertensives in Heart Failure Prognosis: Leveraging Composite Clinical Endpoints and Biomarkers from Electronic Health Records. BCB (2023)
Advait Balaji, Yunxi Liu, Michael G. Nute, Bingbing Hu, Anthony D. Kappell, Danielle S. Lesassier, Gene D. Godbold, Krista Ternus, Todd J. Treangen
SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens. BCB (2023)
Lei Chen, Junhao Su, Zhenxian Zheng, Tak Wah Lam, Ruibang Luo
Large-scale Dataset and Effective Model for Variant-Disease Associations Extraction. BCB (2023)
Zijia Tang, Tonglin Zhang, Qianqian Song, Jing Su, Baijian Yang
PINet: Privileged Information Improve the Interpretablity and generalization of structural MRI in Alzheimer's Disease. BCB (2023)
Felix Quintana, Todd J. Treangen, Lydia E. Kavraki
Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence. BCB (2023)
Arun Nampally, Joseph Kim, Eric Proffitt, Eugene Palovcak, Alix Lacoste
Reference-Free Imputation of Targeted Next-Generation Sequence Datasets. BCB (2023)