IICD Newsletter August 2021

August 02, 2021
August 2nd, 2021
IICD Awards at the 2021 ICML Workshop on Computational Biology
Herbert and Florence Irving Institute for Cancer Dynamics Contributed-Talk Awardees: 
Berk Alpay (left) and Khalil Ouardini (right)
  The Workshop for Computational Biology (WCB) is part of the larger International Conference on Machine Learning (ICML). Originally initiated in 2016 by Elham Azizi, Herbert & Florence Irving Assistant Professor of Cancer Data Research, Irving Institute for Cancer Dynamics and Assistant Professor, Department of Biomedical Engineering, and Sandhya Prabhakaran, Applied Research Scientist at the Integrated Mathematical Oncology Department (Moffit Cancer Center), WCB has been part of ICML every year since. The workshop aims to showcase how recent advances in machine learning and computation can be applied to biological questions and address the large complex datasets generated in multi-omics, cancer biology, or drug discovery for instance. Promoting interdisciplinary research, WCB connects machine learning researchers spanning a wide range of specialties, including computational genomics, neuroscience, metabolomics, proteomics, bioinformatics, cheminformatics, pathology, radiology, evolutionary biology, population genomics, phenomics, ecology, cancer biology, causality, etc.
  This year, WCB was held virtually on July 24th, 2021. The workshop featured invited talks by Mathieu Blanchette (Associate Professor and Director of School of Computer Science at McGill University), Quaid Morris (Group Leader at Memorial Sloane Kettering Cancer Center), Carola-Bibiane Schönlieb (Professor of Applied Mathematics and Head of the Cambridge Image Analysis Group at the University of Cambridge) and Kristin Swanson (Vasak and Anna Maria Polak Professor in Cancer Research and Vice-Chair of Neurosurgery at the Mayo Clinic).
A 41-members Program Committee selected 67 submissions, resulting into 4 contributed talks, 7 highlights of published work, 10 spotlights, and 3 poster sessions including a total of 29 posters. The Chan Zuckerberg Initiative, Columbia Irving Institute for Cancer Dynamics, Python Software Foundation, Moffitt Cancer Center and JetBrains sponsored 4 Best Paper Awards, 3 Best Posters Awards and 45 Diversity Fellowships overall. 

  In particular, the Irving Institute for Cancer Dynamics sponsored two Contributed Talk Awards (selected among the Best Papers) and funded 20 Diversity Fellowships. The
Herbert and Florence Irving Institute for Cancer Dynamics Contributed-Talk Awards were presented to Berk Alpay (PhD student in the Systems, Synthetic, and Quantitative Biology PhD program at Harvard University) for the paper titled “Bayesian Mutation-Selection Model of Evolutionary Constraints on Coding Sequences” and Khalil Ouardini (PhD student at UC Berkeley) for the paper titled “Reconstructing Unobserved Cellular States from Paired Single-Cell Lineage Tracing and Transcriptomics Data”. 
IICD Welcomes Two New Staff Members As Part Of The Administrative Team:
Reed Black, Administrative Coordinator & Victor Salloum, Business Manager
Reed Black's headshotReed Black is a recent transplant from Atlanta, GA. During his time in Atlanta, Reed worked for the Dekalb County Public Library system. He started as a part time shelver and ended as the Circulation Supervisor for the County Line-Ellenwood branch which he helped open in 2019. Reed is a graduate from Ringling College of Art and Design with a Bachelor in Illustration. When Reed isn't at IICD, he is in Brooklyn working on his first Graphic Novel and taking care of his very spoiled cat.
Victor SallVictor Salloum's headshotoum is responsible for administering IICD's budget and daily financial operations. Victor works closely with Dr. Sophie Thuault-Restituito, Chief of Staff, to execute all necessary financial reporting and planning. He brings over 10 years of accounting and financial analysis experience. Prior to joining IICD, Victor managed the Accounts Payable operations at Columbia Business School. Victor received his B.S. in Accounting from The College of New Jersey and completed a M.S. degree in Nonprofit Management from Columbia University School of Professional Studies in 2020.
IICD Researchers in the News
Headshots of Elham Azizi (left) and Itsik Pe'er (right)
“What Machines Can Learn from Genes” in Columbia Engineering Magazine highlights the research by IICD Faculty Elham Azizi (Herbert & Florence Irving Assistant Professor of Cancer Data Research, Irving Institute for Cancer Dynamics and Assistant Professor of Biomedical Engineering) and IICD Associate Itsik Pe’er (Associate Professor of Computer Science).
Read More
IICD Team at Velocity: Columbia's Ride to End Cancer
Screenshot of a zoom meeting with the 5 members of the IICD teamAs announced in the July newsletter, IICD decided to take part in Velocity: Columbia’s Ride to End Cancer this year by organizing a team. Our Institute was created 3 years ago with the mission to focus on the interplay between mathematical sciences and cancer research, collaborating across disciplinary boundaries to develop aspects of science, engineering and the humanities that can improve understanding of cancer biology, origins, treatment and prevention. As we grow, we feel now ready to support Your Velocity and created a team this year! Our team will run, bike, walk and may even be dancing! Help us support the life-saving research and comprehensive care for patients and their families at the Herbert Irving Comprehensive Cancer Center (HICCC) by joining our team or donating.
Visit the IICD Team Page
Recent Publications
Clonal Fitness Inferred from Time-Series Modelling of Single-Cell Cancer Genomes
Salehi et al., Nature 2021, 595, 585-590. From IICD affiliates Samuel Aparicio and Sohrab P. Shah, & the IMAXT Consortium (including IICD Director Simon Tavaré, IICD postdocs Ignacio Vázquez-Garcia and Khanh N. Dinh, and IICD graduate student Russel Kunes)For more information, click here.

Hypothesis Testing for the Covariance Matrix in High-Dimensional Transposable Data with Kronecker Product Dependence Structure. 
Touloumis et al. Statistica Sinica 2021, 31, 1309-1329. From IICD Director 
Simon Tavaré.
Promotion of Cholangiocarcinoma Growth by Diverse Cancer-Associated Fibroblast Subpopulations
Affo et al.Cancer Cell 2021, 39(6), 866-882. With the participation of IICD associates Brent Stockwell and Jellert Gaublomme.
Job Opportunities
Postdoc opening with Professors Mijo Simunovic and Elham Azizi
The Simunovic and Azizi labs are jointly seeking a postdoctoral scholar with experimental or computational training in any field of quantitative biosciences, including chemical and biological engineering, computational biology or (bio)physics, to take part in studying the basic biology of signaling, patterning, and morphogenesis in the context of human organ development and disease, including cancer. Learn more herePlease email Elham Azizi ([email protected]) and Mijo Simunovic ([email protected]) with your CV and contacts for three letters of reference.

Joint Postdoc opening in the ZMBBI and IICD
IICD and the Peterka lab at the Mortimer B. Zuckerman Mind Brain Behavior Institute are seeking a highly motivated postdoctoral research scientist to spearhead a collaborative research project focused on the application and development of advanced optical imaging instrumentation and methods for spatially resolved tissue imaging and -omics primarily in tumors.  The postdoctoral research scientist will oversee developing new approaches to image and interrogate the tumor microenvironment with single-cell resolution. The ideal candidate has prior experience with advanced microscopy and optomechanical integration, as well as image processing and analysis. Learn more here. Please contact [email protected] and [email protected] if interested.

Postdoctoral positions available - Modeling Immunological Memory
Immunological memory is a complex system that is highly dynamic in time and space, involving multiple cell populations that compete, self-renew, turn over, and shift in phenotype and repertoire diversity over a person’s lifetime. The Yates group has openings for postdoctoral positions, using mathematical and computational methods to characterize the dynamic structure of T and B cell memory in various settings. Expertise in immunology is an advantage but not required. See more about this opportunity here, or to make an informal inquiry, email [email protected] 
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