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Bioinformatics Training and Education Program

BTEP Distinguished Speakers Seminar Series

2024 Seminar Series

A More Comprehensive Landscape of RNA Alterations in Cancer with Long-read Sequencing

  • When: June 6, 2024
  • Delivery: Online
  • Presented By: Angela Brooks, Ph.D., (UCSC)
  • The Brooks Lab developed a computational tool called FLAIR (Full-Length Alternative Isoform Analysis of RNA) to produce confident transcript isoforms from long-read RNA-seq data with the aim of alternative isoform detection and quantification. With an increase in the usage of long-read RNA-seq, there is a growing need for a systematic evaluation of this approach. We are part of an international community effort called the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) to perform such an evaluation. The Brooks Lab is extending FLAIR to incorporate sequence variation, RNA editing, and RNA modification in isoform detection as well as detection of complex gene fusions from long-read sequencing data.

     
    Meeting number:
    2311 656 4503
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Statistical Methods for Single-Cell RNA-Seq Analysis and Spatial Transcriptomics

  • When: June 20, 2024
  • Delivery: Online
  • Presented By: Rafael Irizarry, Ph.D. (Harvard)
  • Dr. Irizarry will share findings demonstrating limitations of current
    workflows that are popular in single cell RNA-Seq data analysis.
    Specifically, he will describe challenges and solutions to dimension
    reduction, cell-type classification, and statistical significance
    analysis of clustering. Dr. Irizarry will end the talk describing some of his
    work related to spatial transcriptomics. Specifically, he will describe
    approaches to cell type annotation that account for presence of
    multiple cell-types represented in the measurements, a common
    occurrence with technologies such as Visium and SlideSeq. He will
    demonstrate how this approach facilitates the discovery of spatially
    varying genes.
    Meeting link:
    https://cbiit.webex.com/cbiit/j.php?MTID=m9dcd9ce21f4fa6b1a8e2d998a88c2c2b 
     
    Meeting number:
    2317 712 9095
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Genomes, Avatars and AI: The Future of Personalized Medicine

  • When: August 8, 2024
  • Delivery: Online
  • Presented By: Olivier Elemento, Ph.D. (Weill Cornell Medicine)
  • The Elemento lab combines Big Data analytics with experimentation to develop entirely new ways to help prevent, diagnose, understand, treat and ultimately cure disease. Our research involves routine use of ultrafast DNA sequencing, proteomics, high-performance computing, mathematical modeling, and artificial intelligence/machine learning. We’re revolutionizing healthcare by developing innovative approaches to better predict, diagnose, treat, and prevent disease to improve clinical care for every patient.  

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    2319 759 4122
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Clinical and Computational Molecular Profiling in Pediatric Cancer Diagnostics

  • When: August 29, 2024
  • Delivery: Online
  • Presented By: Elaine Mardis, Ph.D. (Nationwide Children's Hospital)
  • Dr. Mardis is an internationally recognized expert in cancer genomics, with ongoing interests in the integrated characterization of cancer genomes, defining DNA-based somatic and germline interactions and RNA-based pathways, and immune microenvironments that lead to cancer onset and progression, specifically involving pediatric cancers. Most recently, her research has been oriented toward translational aspects of cancer genomics, specifically identifying how the cancer genome changes with treatment, including acquired resistance, the use of genomics in understanding immune therapy response, and the clinical benefit of cancer molecular profiling in the pediatric setting.

    Alternative Meeting Information:
    Meeting number:
    2312 714 2024
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Rachel O'Neill

  • When: September 12, 2024
  • Delivery: Online
  • Presented By: Rachel O'Neill, Ph.D. (Univ. of Connecticut)
  • Dr. O'Neill's research programs employ molecular genetics, genomics and computational approaches to study the mechanisms that maintain, and disrupt, genome stability with a particular focus on repetitive elements. Projects include studying: retroelement transcription and centromere function; novel small RNA biogenesis pathways; and global chromosome and genome changes during instability (such as in cancer and hybrid dysgenesis). In addition, we use a diverse set of rapidly evolving next generation sequencing (NGS) technologies and novel library preparation and computational methodologies for drafting and characterizing genome sequences in efforts to establish broad eukaryotic species as models for studying genome biology. Recently, Dr. O'Neill's lab has expanded their efforts towards applying broad NGS techniques to both model and non-model systems to understand the dynamic response of the genome to environmental queues, such as global warming.

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    2315 524 3558
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Building and Rebuilding the Vertebrate Retina, One Cell at a Time

  • When: November 7, 2024
  • Delivery: Online
  • Presented By: Seth Blackshaw, Ph.D. (Johns Hopkins)
  • Dr. Blackshaw's work examines the molecular basis of neuronal and glial cell fate specification and survival, focusing on characterizing the network of genes that control specification of different cell types within the retina and hypothalamus, two structures that arise from the embryonic forebrain.  The ultimate goal is to use insights gained from learning how individual cell types are specified to understand how these cells contribute to the regulation of behavior, and how they can be replaced in neurodegenerative disease.

    Meeting number:
    2312 437 6963
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Pre-clinical Evaluation of Targeted Therapies for Pediatric Cancer

  • When: November 21, 2024
  • Delivery: Online
  • Presented By: Carol Bult, Ph.D., (The Jackson Lab)
  • The primary theme of Dr. Bult's personal research program is “bridging the digital biology divide,” reflecting the critical role that informatics and computational biology play in modern biomedical research. Dr. Bult is a Principal Investigator in the Mouse Genome Informatics (MGI) consortium that develops knowledge-bases to advance the laboratory mouse as a model system for research into the genetic and genomic basis of human biology and disease. Recent research initiatives in Dr. Bult's research group include computational prediction of gene function in the mouse and the use of the mouse to understand genetic pathways in normal lung development and disease.

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Multimodal Data Integration: From Biomarkers to Mechanisms Archived

  • When: May 23, 2024
  • Delivery: Online
  • Presented By: Caroline Uhler, Ph.D. (MIT)
  • An exciting opportunity at the intersection of the biomedical sciences and machine learning stems from the growing availability of large-scale multi-modal data (imaging-based and sequencing-based, observational and perturbational, at the single-cell level, tissue-level, and organism-level). Traditional representation learning methods, although often highly successful in predictive tasks, do not generally elucidate underlying causal mechanisms. Dr. Uhler will present initial ideas towards building a statistical and computational framework for causal representation learning and its applications towards identifying novel disease biomarkers as well as inferring gene regulation in health and disease.

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    2312 523 4308
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Engineering Serendipity: Computational Methods for Large-Scale Data Extraction Archived

  • When: April 11, 2024
  • Delivery: Online
  • Presented By: Casey Greene, Ph.D., (CU Anschutz)
  • Informaticians aim to bring the right information to the forefront at the right time to improve decision-making. Dr. Greene's  lab develops computational methods that integrate distinct large-scale datasets to extract the rich and intrinsic information embedded in such integrated data. Dr. Greene will discuss how this can reveal underlying principles of an organism’s genetics, its environment, and its response to that environment. Dr. Greene will also discuss work in the CU Anschutz Center for Personalized Medicine that brings genetics to the point of care.

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    2304 252 4992
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2023 Seminar Series

Translating Single Cell Genomics for use in Patients after Blood and Marrow Transplantation Archived

  • When: November 2, 2023
  • Delivery: Online
  • Presented By: Scott Furlan (Fred Hutchinson Cancer Center)
  • In this seminar, Dr. Furlan will share data using single cell genomic technologies after hematopoietic cell transplantation including the molecular approaches and computational tools they have used and developed as they relate to this field.

    Meeting number:
    2302 366 1547
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CANCELLED EVENT: Precisely Practicing Medicine from 700 Trillion Points of Data Archived

  • When: October 5, 2023
  • Delivery: Online
  • Presented By: Atul Butte, MD (UCSF)
  • There is an urgent need to take what we have learned in our new data-driven era of medicine, and use it to create a new system of precision medicine, delivering the best, safest, cost-effective preventative or therapeutic intervention at the right time, for the right patients.  Dr. Butte's teams at the University of California build and apply tools that convert trillions of points of molecular, clinical, and epidemiological data -- measured by researchers and clinicians over the past decade and now commonly termed “big data” -- into diagnostics, therapeutics, and new insights into disease.  Dr. Butte, a computer scientist and pediatrician, will highlight his center’s recent work on integrating electronic health records data from over 8 million patients across the entire University of California, and how analytics on this “real world data” can lead to new evidence for drug efficacy, new savings from better medication choices, and new methods to teach intelligence – real and artificial – to more precisely practice medicine.

     
     
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Hematopoietic stem cell-intrinsic and -extrinsic contribution to aging and clonal hematopoiesis Archived

  • When: September 14, 2023
  • Delivery: Online
  • Presented By: Jennifer Trowbridge (The Jackson Lab)
  • While there is a positive correlation between cancer and aging, the mechanisms underlying this relationship remain unclear. Clonal hematopoiesis, a benign condition that is both associated with aging and predisposes to increased risk of development of blood cancers, presents an opportunity to understand the connection between cancer and aging. This seminar will discuss emerging discoveries of mechanisms acting within the hematopoietic stem cells as well as alterations in the bone marrow microenvironment that promote clonal hematopoiesis and transformation to blood cancers.

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The Power of Connection: How the Cancer Research Data Commons enables researchers to connect data, computational tools, and collaborators to accelerate discovery Archived

  • When: May 4, 2023
  • Delivery: Online
  • Presented By: Brandi Davis-Dusenbery (Velsera)
  • The National Cancer Insitute (NCI) Cancer Research Data Commons (CRDC) includes petabytes of genomic, proteomic, imaging and other data that can be immediately accessed and analyzed by approved users in a secure cloud environment. In this webinar, attendees will learn how the CRDC is transforming cancer research by streamlining collaboration, democratizing access to data and increasing accessibility of complex computational algorithms. We will include a live demonstration of the Seven Bridges Cancer Genomics cloud as well as case studies of research performed in the CRDC. 
     
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AI Models of Cancer in Precision Medicine: Trey Ideker Archived

  • When: March 30, 2023
  • Delivery: Online
  • Presented By: Trey Ideker (UCSD)
  • AI Models of Cancer and Precision Medicine: Building a Mind for Cancer

    The long-term objective of the Ideker Lab is to create artificially intelligent, mechanistic models of cancer and neurodegenerative diseases for translation of patient data to precision diagnosis and treatment. We seek to advance this goal by addressing fundamental questions in the field: What are the genetic and molecular networks that promote disease, and how do we best chart these? How do we use knowledge of these networks in intelligent systems for predicting the effects of genotype on phenotype? – Ideker Lab, https://idekerlab.ucsd.edu/research/cancer/

    Meeting number:
    2301 489 7073
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    Cohost:
    Alex Emmons; Amy Stonelake; Desiree Tillo; Peter Fitzgerald; Joe Wu; Carl McIntosh
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    This webinar will be recorded and made available on the BTEP web site: https://bioinformatics.ccr.cancer.gov/btep/btep-video-archive-of-past-classes/ within 48 hours after the event ends. 

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2022 Seminar Series

A 500 Year Plan for Genetics, Epigenetics and Cell Engineering Archived

  • When: September 22, 2022
  • Delivery: Online
  • Presented By: Christopher Mason (Weill Cornell Medicine)
  • The avalanche of easy-to-create genomics data has impacted almost all areas of medicine and science, from cancer patients and microbial diagnostics to molecular monitoring for astronauts in space. In this lecture, new discoveries from RNA- and DNA-sequencing with the FDA’s SEQC study show the ability of single-molecule methods to reveal rare alleles and provide more comprehensive epigenomics maps of patients and cancers. Also, recent technologies and algorithms from our laboratory and others demonstrate that an integrative, cross-kingdom view of patients (precision metagenomics) holds unprecedented biomedical potential to discern risk, improve diagnostic accuracy, and to map both genetic and epigenetic states, as well as clonal changes in mutations with clonal hematopoiesis. Finally, these methods and molecular tools work together to guide comprehensive, longitudinal, multi-omic views of human astronaut physiology and biology in the NASA Twins Study and several other missions with SpaceX and Axiom, which lay the foundation for future, long-duration spaceflight, including sequencing, quantifying, and engineering genomes to survive on other planets over the next 500 years (https://mitpress.mit.edu/books/next-500-years).

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Decoding Breast Cancer Progression with Single Cell Genomics Archived

  • When: July 14, 2022
  • Delivery: Online
  • Presented By: Nicholas Navin (MD Anderson Cancer Center)
  • The efforts of our laboratory are split evenly between experimental and computational biology.  We develop new experimental methods to sequence single cells and isolate rare subpopulations and develop new analytical approaches to detect variants and apply statistical methods to these data sets.  We focus mainly on breast cancer to understand the role of clonal diversity in the evolution of invasion, metastasis and response to chemotherapy.  We are also using these tools to study rare tumor cell subpopulations including circulating tumor cells and cancer stem cells.  Our goal is to understand the role of clonal diversity in tumor evolution so that we can exploit this diversity for therapeutic vulnerabilities and improve diagnostic tools and the early detection of cancer.  We fully expect that applying these tools to human patients will lead to reduced morbidity in breast cancer.

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Mapping the Human Body One Cell at a Time Archived

  • When: June 16, 2022
  • Delivery: Online
  • Presented By:
  • Sarah Teichmann is co-founder and principal leader of the Human Cell Atlas (HCA) international consortium. The International Human Cell Atlas initiative aims to create comprehensive reference maps of all human cells to further understand health and disease.

    The 37 trillion cells of the human body have a remarkable array of specialized functions, and must cooperate and collaborate in time and space to construct a functioning human. In this talk I will describe my lab’s efforts to understand this cellular diversity through a programme of cell atlasing. Harnessing cutting edge single cell genomics, imaging and computational technologies, we investigate development, homeostasis and disease states, at scale and in 3D, with a particular focus on immunity. I will illustrate the relevance of cell atlas-ing for engineering organoids and regenerative medicine, and will share new results providing insights into pacemaker cells from the sinoatrial node of this heart. Overall I hope to illustrate the power of single cell approaches in unlocking fundamental knowledge about the human body.

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Realizing Data Interoperability Across Basic Research, Clinical Care, and Patients Archived

  • When: April 21, 2022
  • Delivery: Online
  • Presented By: Melissa Haendel (CU Anschutz)
  • Making data reusable for discovery and shared analytics across domains is a laborious, specific-skill requiring task that most data providers do not have the resources, expertise, or perspective to perform. Equally challenged are the data re-users, who function in a landscape of bespoke schemas, formats, and coding – when they can get past understanding the licensing and access control issues. Making the most of our collective data requires partnerships between basic researchers, clinicians, patients, and informaticians, as well as sophisticated strategies to address a myriad of interoperability issues. This talk will review different communities endeavors towards these ends from across the translational spectrum.

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Integrated Analysis of Single Cell Data Across Technologies and Modalities Archived

  • When: February 17, 2022
  • Delivery: Online
  • Presented By: Rahul Satija (NYU)
  • Our goal is to understand how cellular heterogeneity encodes the molecular structure, function, and regulation of complex biological systems. Primarily using single cell genomics, we analyze systems by profiling their most fundamental units individually – a ‘bottom-up’ approach that allows us to study how diverse groups of cells work together to drive biological processes and behaviors. – Satija Lab

    Since Dr. Satija will be presenting unpublished work in this webinar, it will not be recorded or distributed.

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