Program

10:30	Kaili Liu, Ashley Hoover, Jacob Adams, Trisha Valero, Coline Furrer, Robert Miller, Yuanhong Sun and Wei Chen Single-cell RNA-sequencing analysis of breast tumor infiltrating lymphocytes treated with localized ablative cancer immunotherapy (abstract)
10:54	Julia Cordes and Jaime Davila Cancer and Tissue Prediction Using Mutational Signatures in Highly Mutated Cancers (abstract)
11:18	Bikram Sahoo, Nikita Jinna, Padmashree Rida, Zandra Pinnix and Alex Zelikovsky Decoding Heterogeneity in Quadruple-Negative Breast Cancer: A Data-Driven Clustering Approach (abstract)
11:42	Ankur Yadav and Daescu Ovidiu A Unified Machine Learning Framework for Multi-subtype Tumour Classification across Diverse Datasets (abstract)
12:06	Sri Lakshmi Bhavani Pagolu, Suba S and Nita Parekh DNA Methylation Based Subtype Classification of Breast Cancer (abstract)

10:30-12:30 Session 2B: CAME Workshop - I

CAME Workshop - I

Chairs:

Pavel Skums and Murray Patterson

Location: OMU Scholars

10:30	Leonid Bunimovich and Athulya Ram Sreedharan Nair Antigenic cooperation and cross-immunoreactivity networks
10:54	Taslim Murad, Sarwan Ali and Murray Patterson Hashed Embeddings: A Promising Technique for Efficient Protein Sequence Representation
11:18	Seth Sims, Yury Khudyakov and Alexander Zelikovsky Assessment of PHRED Score Characteristics in Illumina MiSeq Amplicon Sequencing
11:42	Sarwan Ali, Haris Mansoor, Prakash Chourasia, Yasir Ali and Murray Patterson Gaussian Beltrami-Klein Model for Protein Sequence Classification: A Hyperbolic Approach
12:06	Fahad Alqahtani, Manee Manee, Badr Al-Shomrani and Ion Măndoiu Mitogenome Assembly from Ultraconserved Elements Sequencing Reads

12:30-13:30 Lunch

Boxed Lunch

Location: OMU Molly Shi Boren Ballroom

13:30-14:30 Session 3: 2nd Keynote Talk

2^nd Keynote Talk

Chairs:

Pavel Skums and Sanguthevar Rajasekaran

Location: OMU Molly Shi Boren Ballroom

13:30

Karen Jonscher and Jacob Friedman

Unraveling the Early-Life Origins of Nonalcoholic Fatty Liver Disease (NAFLD) Using Multi-'Omics Approaches (abstract)

14:30-16:30 Session 4A: ICCABS - Deep Learning and Predictive Models

ICCABS- Deep Learning and Predictive Models

Chairs:

Ion Mandoiu and Sanguthevar Rajasekaran

Location: OMU Regents & Associates

14:30	Siqi Chen, Wenkang Wang, Ruiqing Zheng and Min Li SpaNN: a flexible deep neural network framework for predicting the transcript distribution of the spatial transcriptomics (abstract)
14:54	Konstantinos Barzas, Shereen Fouad, Gainer Jasa and Gabriel Landini An Explainable Deep Learning Framework for Mandibular Canal Segmentation from Cone Beam Computed Tomography volume (abstract)
15:18	Bin Li, Hongchang Gao and Xinghua Shi FedDP: Secure Federated Learning with Differential Privacy for Disease Prediction (abstract)
15:42	Ayush Chaturvedi, Guohua Cao and Wu-Chun Feng Optimizing Deep Learning for Biomedical Imaging (abstract)
16:06	Sumit Kumar Jha, Pranav Sinha and Sunny Raj Automated Formalization of Biological Model Properties into Temporal Logics using Large Language Models (abstract) PRESENTER: Sunny Raj

14:30-16:30 Session 4B: CAME Workshop - II

CAME Workshop - II

Chairs:

Pavel Skums and Mukul Bansal

Location: OMU Scholars

14:30	Justin Su, Viorel Munteanu, Victor Gordeev, Khooshbu Patel, Nicolae Drabcinski, Oksana Zlenko, Maryna Kit, Yidian Xu, Pooja Jaiswal, Alex Zelikovsky and Serghei Mangul A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
14:54	Rahul Singh Tracking and modeling the dynamics of evolving SARS-CoV-2 Variants
15:18	Alexander Kirpich Clustering-Based Multi-Characteristic Comparative Analysis of COVID-19 Epidemiology in Europe
15:42	Pavel Skums Early detection of emerging viral variants with altered phenotypes using viral epistatic networks
16:06	Francesco Tomasella and Cinzia Pizzi On Multi-Phase Metagenomics Reads Binning (abstract)

16:30-17:00 Coffee Break

Location: OMU Molly Shi Boren Ballroom

17:00-18:30 Session 5: Poster Session

Poster Session

Chair:

Marmar Moussa

Location: OMU Molly Shi Boren Ballroom

Varuni Sarwal, Seungmo Lee, Jianzhi Yang, Sriram Sankararaman, Mark Chaisson, Eleazar Eskin and Serghei Mangul

VISTA: An integrated framework for structural variant discovery (abstract)

Michael Yu, Steven Wilson and Sina Khanmohammadi

Genetic Predisposition to Alcoholism Significantly Alters the Functional Connectivity of the Brain (abstract)

Hsin-Hao Chen and Chung-Chin Lu

A Model for Elucidating the Single Molecule Synthesis Process through Temporal Information (abstract)

Justin Su, Viorel Munteanu and Serghei Mangul

A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater (abstract)

Daniel Rosenberg and Marmar Moussa

Role of walnut-derived urolithins in reducing colonic inflammation in a patient cohort elucidated by an integrated omics analysis (abstract)

Marmar Moussa and Sriram Boddeda

Computational tumor progression analysis via seriation based trajectory inference (abstract)

Kyle Song

Predicting Antibiotic Metabolites with One and Two-Steps in Silico Biotransformations to Support Identification of Unknown Chemicals in Exposome and Metabolome Studies (abstract)

Deepanshu Mody

Exploring Protein Design Landscapes with Semi-Supervised Adaptive Sampling (abstract)

Lucas Otavio L. Silva, Karine Marques Hara, Pedro Henrique Mendes de Paula, Alexandre Rossi Paschoal and Fabrício Martins Lopes

A Simple and Interpretable Deep Learning Model for Diagnosing Pneumonia from Chest X-Ray Images (abstract)

Hua Zhong, Kathryn Burge and Hala Chaaban

Network-Based Bioinformatics Highlights Broad Importance of Human Milk Hyaluronan (abstract)

Shashank Pathak and Guohui Lin

mRNA stability prediction (abstract)

Reza Roofegari Nejad, Pranay Julu and Sahar Hooshmand

PHViT4Lung: Parallel Hybrid Vision Transformers Augmented by Transfer Learning to Enhance Lung Cancer Diagnosis (abstract)

Justin Harris, Andrew Fagg, Dee Wu and Karla Rodgers

Integrating Neural Networks into DNA Sequence-Based Predictions of RSS Functionality and Activity Level

Rachel Bennett and Talayeh Razzaghi

Fast Multi-level Neural Networks to Overcome Bias in Healthcare Applications (abstract)

Aanuoluwa Adekoya and Carolyn Ibberson

Investigating Microbial Community Functions in Chronic Bacterial Infections (abstract)

Marmar Moussa

A computational framework for identifying TCell Receptor specificity in single cell resolution (abstract)

18:30-20:30 Networking Event

Networking Event

Location: OMU Beaird Lobby & Lounge

Tuesday, December 12th

View this program: with abstracts session overview talk overview

08:00-09:00 Registrations - Coffee & Pastry

Registration

Location: OMU Molly Shi Boren Ballroom

09:00-10:00 Session 6: 3rd Keynote Talk

3^rdKeynote Talk

Chairs:

Marmar Moussa and Sanguthevar Rajasekaran

Location: OMU Molly Shi Boren Ballroom

09:00

Jie Chen

Computational and modeling aspects of analyzing high-throughput genomic data (abstract)

10:00-10:30 Coffee Break

Coffeee Break

Location: OMU Molly Shi Boren Ballroom

10:30-12:30 Session 7A: ICCABS - Sequence Analysis

ICCABS - Sequence Analysis

Chairs:

Pavel Skums and Sanguthevar Rajasekaran

Location: OMU Regents & Associates

10:30	Dottie Yu, Ram Ayyala, Sarah Sadek, Hafsa Farooq, Likhitha Chittampalli, Junghyun Jung, Jieting Hu, Tianze Tao, Ryan Alomair, Sungmin Park, Austin Nguyen, Nicholas Mancuso, Jong Wha Joo, Reid Thompson, Houda Alachkar and Serghei Mangul A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data
10:54	Paola Bonizzoni, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino and Rosalba Zizza Identification of Chimeric RNAs: a novel machine learning perspective (abstract)
11:18	Ahmed Soliman and Sanguthevar Rajasekaran A Novel String Map-Based Approach for Distance Calculations with Applications to Faster Record Linkage (abstract)
11:42	Sarwan Ali, Haris Mansoor, Prakash Chourasia, Imdadullah Khan and Murray Patterson Preserving Hidden Hierarchical Structures: Poincaré Distance for Enhanced Genomic Sequence Analysis
12:06	Arnab Ganguly, Daniel Gibney and Sharma V. Thankachan On the Hardness of Wildcard Pattern Matching on de Bruijn Graphs (abstract)

10:30-12:30 Session 7B: ASI Workshop - I

ASI Workshop - I

Chairs:

Marmar Moussa and Ion Mandoiu

Location: OMU Scholars

10:30	Wei Chen Single-cell RNA sequencing reveals the atlas of a breast tumor microenvironment and the remodeling by photo-immunotherapy
10:54	Alexandra "Sasha" Gavryushkina, Holly Pinkney, Sarah Diermeier and Alex Gavryushkin Single cell RNA phylogenetics of cancer
11:18	Serghei Mangul Adaptive receptor repertoire profiling methods for RNA sequencing
11:42	Aanuoluwa Adekoya and Carolyn Ibberson Investigating Microbial Community Functions in Chronic Bacterial Infections (abstract)
12:06	Abdulrafeh Naqash and Hassan Abushukair Association of baseline tumor-specific neoantigens and CD8+ T infiltration with immune-related adverse events secondary to immune checkpoint inhibitors

12:30-13:30 Lunch

Boxed Lunch

Location: OMU Molly Shi Boren Ballroom

13:30-15:30 Session 8A: ICCABS - Machine Learning Models

ICCABS - Machine Learning Models

Chairs:

Pavel Skums and Murray Patterson

Location: OMU Regents & Associates

13:30	Namitha Pais, Nalini Ravishanker, Sanguthevar Rajasekaran and George Weinstock Repeated Measures Latent Dirichlet Allocation for Longitudinal Microbiome Analysis (abstract)
13:54	Chen Song, Yuzhou Chen, Huanmei Wu and Xinghua Shi GenoDiffusion: Conditional Denoising Diffusion Model for Genomic Data Augmentation (abstract)
14:18	Aysegul Bumin, Kejun Huang and Tamer Kahveci PartialFibers: An efficient method for predicting Drug-Drug Interactions (abstract)
14:42	Hanxia Li and Sixia Chen Machine Learning Application for Predicting Smoking Cessation Among US Adults: An Analysis of Waves 1-5 of the PATH Study (abstract)
15:06	Arghya Kusum Das ParMEC: A Set of Algorithms for Parallel Metagenomic Error Correction (abstract)

13:30-15:30 Session 8B: ASI Workshop - II / CASCODA Workshop - I

ASI Workshop II / CASCODA Workshop I

Chairs:

Ion Mandoiu and Marmar Moussa

Location: OMU Scholars

13:30	Samson Weiner, Bingjun Li, Hari Patchigulla and Sheida Nabavi Improved inference of single-cell haplotype-aware copy numbers in cancer
13:54	Walker Hoolehan, Adeline Machalinski and Willard Freeman Epigenetic regulation of endogenous viral elements in the aging brain
14:18	Michael K.B Ford, Ananth Hari and Cenk Sahinalp Genotyping complex immune loci using integer linear programming
14:42	Russell Schwartz Incorporating structural variation into single-cell clonal lineage inference
15:06	Siyuan Luo, Pierre-Luc Germain, Mark Robinson and Ferdinand von Meyenn Benchmarking computational methods for single-cell chromatin data analysis

15:30-16:00 Coffee Break

Coffee Break

Location: OMU Molly Shi Boren Ballroom

16:00-17:36 Session 9A: ICCABS - Deep Learning and Biomedical Imaging

ICCABS - Deep Learning and Biomedical Imaging

Chairs:

Sanguthevar Rajasekaran and Pavel Skums

Location: OMU Regents & Associates

16:00	Qinggong Tang Enhancing Biomedical Research Using Novel Optical Imaging Technologies and Deep Learning (abstract)
16:24	Xihan Qin and Li Liao Improving Disease Comorbidity Prediction with Biologically Supervised Graph Embedding (abstract)
16:48	Armen Kasparian, Guohua Cao and Wu-Chun Feng A 3D Deep Learning Architecture for Denoising Low-Dose CT Scans (abstract)
17:12	Suba S and Nita Parekh Lightweight and Generalizable Model for COVID-19 Detection Using Chest Xray Images (abstract)

16:00-17:36 Session 9B: CASCODA Workshop - II

CASCODA Workshop - II

Chairs:

Ion Mandoiu and Murray Patterson

Location: OMU Scholars

16:00	Mohsen Sharifitabar, Shiva Kazempour Dehkordi, Javad Razavian, Sogand Sajedi, Soroosh Solhjoo and Habil Zare A deep neural network to de-noise single-cell RNA sequencing data (abstract)
16:24	Akshay Juyal, Zahra Tayebi, Alex Zelikovsky, Simone Ciccolella, Gianluca Della Vedova and Murray Patterson Plastic: An easy to use and modular tool for designing tumor phylogeny reconstruction pipelines
16:48	Marmar Moussa Computational framework for spatial omics analysis of colon polyp tissue
17:12	Vrishabhadev Sathish Kumar A Computational Atlas for Transcriptomic Exploration of M. buryatense Using Unsupervised Machine Learning and Interactive Data Visualization (abstract)

18:30-21:30 Banquet

Banquet

Location: OMU Molly Shi Boren Ballroom

Wednesday, December 13th

View this program: with abstracts session overview talk overview

08:00-08:30 Coffee & Pastry

Location: OMU Regents & Associates

08:30-10:30 Session 10A: ICCABS - Neural Networks and Neuroscience

ICCABS - Neuroscience session, including topics in Neuroscience and Neural Networks.

Chairs:

Sanguthevar Rajasekaran and Pavel Skums

Location: OMU Scholars

08:30	Sean Nguyen, Mohammad Amin Basiri and Sina Khanmohammadi Multilayer Network Analysis of Brain Signals for Detecting Alzheimer’s Disease (abstract)
08:54	Emma Stubby, Seyed Majid Razavi and Sina Khanmohammadi Functional Connectivity Disruptions in Alzheimer’s Disease: A Maximum Flow Perspective (abstract)
09:18	Chu-Yu Cheng and Chung-Chin Lu Exploring a Solution Curve in the Phase Plane for Extreme Firing Rates in the Izhikevich Model (abstract) PRESENTER: Chu-Yu Cheng
09:42	Chenyu Zhang and Dong-Guk Shin AFA: Abstract Functional Analysis Identifies New Microglial Subtypes at Single Cell Level in Alzheimer’s Disease (abstract)
10:06	Alice Burghard How to Record a Phantom Sound - Tinnitus Assessment via Electrophysiology (abstract)

08:30-10:30 Session 10B: CANGS Workshop - I

CANGS Workshop - I

Chairs:

Mukul Bansal and Ion Mandoiu

Location: OMU Regents & Associates

08:30	Samson Weiner and Mukul S. Bansal Towards improved reconstruction of single-cell copy number phylogenies
08:54	Bingjun Li and Sheida Nabavi Single-cell Multiomics Clustering Using Graph Embedded Contrastive Learning
09:18	Dottie Yu, Ram Ayyala, Hafsa Farooq, Sarah Sadek, Junghyun Jung, Jieting Hu, Tienze Tao, Ryan Alomair, Likhitha Chittampalli, Sungmin Park, Austin Nguyen, Nick Mancuso, Jong Wha Joo, Reid Thompson, Abhinav Nellore, Houda Alachkar and Serghei Mangul A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data (abstract)
09:42	Seungmo Lee, Varuni Sarwal, Jianzhi Yang, Sriram Sankararaman, Mark Chaisson, Eleazar Eskin and Serghei Mangul VISTA: An integrated framework for structural variant discovery
10:06	Hafsa Farooq, Daniel Novikov, Akshay Juyal and Alex Zelikovsky Genetic Algorithm with Evolutionary Jumps (abstract)

10:30-10:45 Coffee Break

Coffee Break

Location: OMU Regents & Associates

10:45-12:45 Session 11: ICCABS / CANGS Workshop - II

ICCABS / CANGS Workshop - II

Chairs:

Pavel Skums and Sanguthevar Rajasekaran

Location: OMU Regents & Associates

10:45	Sivaramakrishnan Lakshmivarahan Role of Data Assimilation in Prediction: Potential applications to Biological and Medical Sciences (abstract)
11:09	Sing-Hoi Sze An exact matching method for 16S rRNA taxonomy classification
11:33	Grigore Boldirev, Nitesh Sharma, Serghei Mangul and Alex Zelikovsky Assessing Microbial Genome Representation Across Various Reference Databases: A Comprehensive Evaluation
11:57	Liqing Zhang A Hybrid Approach for Antibiotic Resistance Gene Characterization: Leveraging Pre-trained Protein Language Models and Alignment-Based Scoring
12:21	Giri Narasimhan, Kalai Mathee and Vitalii Stebliankin Multiomics, Causality, and Longitudinal microbiomics

12:45-13:30 Closing Remarks and Lunch

Lunch (Fajita bar) and Closing Remarks

Location: OMU Regents & Associates