To view the seminar recording, please click here Talk Title: Cellular plasticity and developmental constraints in tumorigenesis and drug resistance Abstract: Cellular plasticity is emerging as an important driving force underlying cancer progression and drug resistance. In this talk, I will discuss the concept of cancer cell states present in the tumor prior to treatment,...Read More

For seminar recording, please click here Talk Title: Comparative spatial omics analysis across length scales Abstract: Spatially resolved omics technologies provide molecular profiling of cells while preserving their organization within tissues. Such technologies provide the opportunity to evaluate spatial molecular comparisons across healthy versus diseased tissues. In this talk, I will highlight two tools my...Read More

For seminar recording, please click here Talk Title: Artificial Intelligence in Precision Oncology Abstract: Precision oncology requires complex biomarkers which are often based on molecular and genetic tests of tumor tissue. For many of these tests, universal implementation in clinical practice is limited. However, for virtually every cancer patient, pathology tissue slides stained with hematoxylin...Read More

For seminar recording, please click here Talk Title: Using T2T-level comparative genomics to study repeat biology Abstract: Mobile elements and highly repetitive regions are potent sources of lineage-specific genomic innovation and are integral to the structure and function of eukaryotic cells. Recent efforts employing long-read based genome assembly, functional and repeat analyses across multiple marsupial...Read More

For seminar recording, please click here Talk Title: Leveraging mass balance and long DNA molecules to study structural variant mutational processes in cancer Abstract: Genome structure, like other physical phenomena, obeys the simple principle of mass balance. I will show how we can apply this principle algorithmically to assess what structural variants (SVs) are missing from...Read More

For seminar recording, please click here Talk Title: Some mysteries about viruses and cancer Abstract: It has been estimated that 15%-20% of human cancers are attributable to infections, mostly by carcinogenic viruses. The incidence varies worldwide, with a majority affecting developing countries. Here, we present a comparative analysis of virus-positive and virus-negative tumors in nine...Read More

For seminar recording, please click here Talk Title: Modern Hopfield Networks for Novel Transformer Architectures  Abstract: Modern Hopfield Networks or Dense Associative Memories are recurrent neural networks with fixed point attractor states that are described by an energy function. In contrast to conventional Hopfield Networks, which were popular in the 1980s, their modern versions have...Read More

For seminar recording, please click here Talk Title: Probabilistic Modeling of Dynamics of the Tumor Microenvironment Abstract: Cancer therapies succeed only in a subset of patients partly due to the heterogeneity of cells across and within tumors. Single-cell and spatial genomic technologies present exciting opportunities to characterize unknown cell types in complex tissues such as...Read More

For Meeting Recording, please click here. Passcode: 27097062 Talk Title: Methods for tumor phenotype classification from circulating tumor DNA Abstract: An accurate diagnosis of the tumor histology is essential for clinical care. Aggressive tumor phenotypes can emerge through subtype changes and lineage plasticity as major mechanisms of treatment resistance in cancer. Therefore, distinguishing tumor phenotypes...Read More