Program Information

Save the date for the first ITCR Trainee Virtual Symposium: May 15-17, 2024

The ITCR Trainee Virtual Symposium will be an opportunity for you to share your work with others, learn about cutting edge cancer informatics technologies, and network with trainees across the ITCR program.

The symposium will be free, and open to trainees in current and former ITCR-funded labs ranging from undergraduate through post-doctoral career stages. Active ITCR PIs will be asked to nominate at least one trainee from their research group as a speaker.

Welcome Keynote Speakers

DAY1: Jill Mesirov, Ph.D

Associate Vice Chancellor for Computational Health Sciences, Professor, Department of Medicine, co-Lead, Structural and Functional Genomics, Moores Cancer Center UC San Diego

DAY 2: Nastaran Zahir, Ph.D.

Branch Director, Cancer Training Branch Center for Cancer Training, National Cancer Institute

DAY 3: Anant Madabhushi, Ph.D., FAIMBE, FIEEE, FNAI

Robert W Woodruff Professor Wallace H. Coulter Department of Biomedical Engineering, and Departments of Radiology & Imaging Sciences, Biomedical Informatics, Urology, Radiation Oncology, Pathology, Computer Science & Informatics and Global Health. Executive Director, Emory Empathetic AI for Health Institute, Emory Empathetic AI for Health Institute, Georgia Institute of Technology and Emory University, Research Career Scientist, Atlanta Veterans Administration Medical Center

Scientific Program

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Please note, the times are Eastern Standard Time (EST)

DAY I. May 15
1:00 PM	Juli Klemm	National Cancer Institute	Opening of the ITCR Trainee Symposium
1:10 PM	Jill Mesirov	University of California San Diego	Keynote lecture: Computational Cancer Genomics: Applications, Methods, and Software
1:50 PM	Suresh S. Ramalingam	Emory University	Welcoming remarks

Omics technologies across the cancer research continuum
Chair: Ramon Ortiz, Ph.D., University of California San Francisco
2:00 PM	Jens Luebeck	University of California San Diego	AmpliconSuite: Analyzing focal amplifications in cancer genomes
2:10 PM	Anderson Bussing	University of South Carolina	FAST-scDECO: a flexible and adaptive scalable tool for single cell differential coexpression analysis
2:20 PM	Ha Nguyen	Auburn University	DSCC: Disease Subtyping using Consensus Network and Multi-omics Data Integration
2:30 PM	Farzan Taj	University of Toronto	A Deep Learning Foundation Model for Predicting Responses to Genetic and Chemical Perturbations in Single Cancer Cells
2:40 PM	Alexander Wenzel	University of California San Diego	Data driven refinement of gene signatures for enrichment analysis and cell state characterization
2:50 PM	BREAK
Chair: Zeynep Kosaloglu-Yalcin, Ph.D., La Jolla Institute for Immunology
3:00 PM	Daniel Bergman	Johns Hopkins University	Integrating multi-omics analyses into agent-based models made easy: the Bioinformatics Walkthrough for PhysiCell
3:10 PM	Sriya Potluri	University of Pennsylvania Perelman School of Medicine	ImmunoPheno: A Data-Driven Bioinformatics Platform for the Design and Analysis of Immunophenotyping Experiments
3:20 PM	Selina Wu	University of California Los Angeles	Improving Tumour Subclonal Reconstruction via Phasing: A Case Study in Hereditary Leiomyomatosis and Renal Cell Cancer
3:30 PM	Jaime Wehr	Johns Hopkins University	Precision oncology decision-support informatics approaches to match actionable genotypes with targeted therapies
3:40 PM	Tushar Mandloi	EMBL-EBI	CancerModels.Org - an open global cancer research platform for patient-derived cancer models.

DAY II. May 16
1:00 PM	Nastaran Zahir	National Cancer Institute	Keynote lecture: NCI Opportunities for Early Career Cancer Researchers

Flash talks
Chair: Debolina Chatterjee, Ph.D., Indiana University
1:40 PM	Ino de Bruijn	Memorial Sloan Kettering Cancer Center	cBioPortal for Cancer Genomics
1:43 PM	My Hoang	Washington University in Saint Louis	pVACsplice: a bioinformatics tool for detecting and prioritizing tumor-specific splicing-derived neoantigen
1:46 PM	Shan He	MD Anderson Cancer Center	Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles
1:49 PM	Zeynep Kosaloglu-Yalcin	La Jolla Institute for Immunology	A meta-analysis of cancer neoantigens curated from the literature
1:52 PM	Kaiyuan Zhu	University of California San Diego	CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
1:55 PM	Helena Winata	University of California Los Angeles	EMulSI-Phy: Efficient Multi-Sample Inference of Cancer Phylogeny
1:58 PM	Zitong Jerry Wang	California Institute of Technology	Generating counterfactual explanations of tumor spatial proteomes to discover therapeutic strategies for enhancing immune infiltration

General informatics resources and platforms
Chair: Debolina Chatterjee, Ph.D., Indiana University
2:00 PM	Lauren Chan	University of Chicago	Expanding Gearbox: LLM and ontology based opportunities to enrich clinical trial mapping
2:10 PM	Jiarui Yao	Boston Children's Hospital, Harvard Medical School	Extraction of Chemotherapy Treatment Timelines from EHR Notes
2:20 PM	Anja Conev	Rice University	EnGens: a computational framework for generation and analysis of representative protein conformational ensembles
2:30 PM	Romanos Fasoulis	Rice University	APE-Gen2.0: Expanding Rapid Class I pMHC Modeling to Post-Translational Modifications and Non-canonical Peptide Geometries
2:40 PM	Erin Wissler Gerdes	University of Iowa	Evaluating Usability and Feasibility of Implementing Cancer Epidemiology Maps for SEER Registry End Users
2:50 PM	Bryan Zhu	New York Genome Center	An Interactive Analysis on Variant Callers and Performance
3:00 PM	BREAK
Chair: Yi Lian, Ph.D., University of Pennsylvania
3:10 PM	Hongyue (Nicole) Chen	Emory University	Discovering targetable Vulnerabilities in Cancer Using the Averon Notebook
3:20 PM	Ariaki Dandawate	Dana Farber Cancer Institute	Latent embeddings of accessible loci for Automatic Cell-Type Annotation in scATAC-seq Data
3:30 PM	Kaelyn Long	City University of New York	Ontology-leveraged metadata harmonization to improve AI/ML application on omics databases
3:40 PM	Marcel Ramos	CUNY School of Public health	terraTCGAdata: accessing and representing TCGA on the AnVIL
3:50 PM	Haoyue Feng	Boston University	Patterns in Flanking Bases of Mutation Signatures

DAY III. May 17
1:00 PM	Anant Madabhushi	Emory University	Keynote lecture: My ongoing career journey in AI and Medicine

Flash talks
Chair: Daniel Bergman, Ph.D., Johns Hopkins Medicine
1:40 PM	Cally Lin	UC Santa Cruz Genomics Institute	Developing and Deploying the UCSC Xena Gene Set Enrichment Analysis Appyter
1:43 PM	Wei Liu	MD Anderson Cancer Center	TCPAplus: An LLM-empowered Chatbot for Analyzing a Large Protein Expression Atlas of Human Cancers
1:46 PM	Yunhui Qi	Iowa State University	Optimizing Sample Size for Statistical Learning in Bulk Transcriptome Sequencing: A Learning Curve Approach
1:49 PM	Azka Javaid	Dartmouth College	Single cell transcriptomics level surface protein abundance estimation using STREAK.
1:52 PM	Debolina Chatterjee	Indiana University School of Medicine	Identification of High-Risk Cells in Spatially Resolved Transcriptomics of Cancer Biopsies Using Deep Transfer Learning
1:55 PM	Phi Le	University of California San Francisco	Prediction of Multi-Class Peptides by T-cell Receptor Sequences with Deep Learning

Image-based approaches
Chair: Daniel Bergman, Ph.D., Johns Hopkins Medicine
2:00 PM	Michael Kong	Case Western Reserve University	Human-in-the-loop deep learning-based segmentation of rectal tumors on MRI
2:10 PM	Saumya Gupta	Stony Brook University	Topological uncertainty for vascular segmentation
2:20 PM	Michael Yao	Stony Brook University	Topology-Guided Vasculature Analysis
2:30 PM	Xinyi Yang	University of Colorado	Learning without Real Data Annotations to Detect Hepatic Lesions in PET Images
2:40 PM	Benjamin Parker	Case Western Reserve University	Intra- and peri-tumoral radiomic features are predictive of pathologic response to multiple neoadjuvant therapy regimen in rectal cancers via pre-treatment MRI
2:50 PM	Harrison Yee	Rensselaer Polytechnic Institute	Utilizing Deep Learning and Channel-Wise Data Fusion for End-to-end Organelle-based Breast Cancer Cell Classification
3:00 PM	BREAK
Clinical and population research
Chair: Alexander Wenzel, Ph.D., University of California San Diego
3:10 PM	Yingjie Qiu	Indiana University	Transparent and Efficient Adaptive Designs for Clinical Trials
3:20 PM	Yi Lian	University of Pennsylvania	A Flexible and Adaptive Framework for High-Dimensional Fairness-Aware Integration of Data from Multiple Sites
3:30 PM	Yiming Zhang	UMass Chan Medical School	Disparities in the Documentation of Social Determinants of Health ICD-10 Z-Codes for Patients Diagnosed with Cancer: An Epic Cosmos Study
3:40 PM	Julia Herriott	Cincinnati Children's Hospital Medical Center	Pilot Testing the User Interface for a Novel Algorithm to Process Electronic Adherence Monitoring Device Data
3:50 PM	Ramon Ortiz	University of California San Francisco	The TPS2TOPAS interface tool for investigating new radiotherapy devices

4:00 PM	Juli Klemm	NIH National Cancer Institute	Closing remarks

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Registration deadline: May 14th, 2024.

The Registration is free. Click here to register now!