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October 2021
QCBio Research Seminar: Giovanni Quinones Valdez (Xiao), Grad student in Bioengineering
TITLE: "scAllele, a versatile tool for the detection and analysis of variants in scRNA-seq." ABSTRACT: Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better…
Find out more »QCBio Research Seminar: Ulzee An (Sankararaman), Grad student in Computer Science
TITLE: "AutoComplete: Deep Learning-based Phenotype Imputation" ABSTRACT: Health data has become increasingly available, vast in scale, and highly missing. For many downstream applications, the ability to accurately impute missing features in health records may tap into additional analytical power which would be unrealized otherwise. While existing imputation methods are applicable, many fall short in one or more aspects of being reliable or scalable in the domain of massive, highly incomplete, and heterogenous population-scale data. We propose AutoComplete, a deep learning-based…
Find out more »November 2021
Bioinformatics/Human Genetics Seminar Series: Anya Prince, Associate Professor of Law, Genetic Cluster, University of Iowa College of Law
“Regulating Insurer Use of Genetic Information” Hosted by Christina Palmer
Find out more »QCBio Research Seminar: Alexander Markowitz (Boutros), Postdoc in Human Genetics
TITLE: "A pan-cancer multi-omic analysis of tumor proliferation." ABSTRACT: The underlying mechanisms of dysregulated cellular proliferation in cancer remain unclear; however, it is hypothesized that specific mutations, mutational signatures, evolutionary trajectories and other global (epi)genomic features may be linked to differing rates of proliferation. In this presentation, I will showcase a landscape analysis of cellular proliferation across primary cancers and cell lines using genome, transcriptome and proteome data from 11,597 primary tumors and 1,804 cell lines across six major consortia. The…
Find out more »QCBio Research Seminar: Ricky Wolff (Garud), Graduate Student in Ecology & Evolutionary Biology
TITLE: "Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome." ABSTRACT: The human gut microbiome is a complex community that harbors substantial ecological diversity at the species level, as well as at the strain level within species. In healthy hosts, species abundance fluctuations in the microbiome community are thought to be stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is…
Find out more »Bioinformatics/Human Genetics Seminar Series: Eimear Kenny, Founding Director, Institute for Genomic Health, Mount Sinai School of Medicine
“Population genetics in an era of genomic health” Hosted by Christa Caggiano
Find out more »QCBio Research Seminar: Guo Xiaohui (Pinter-Wollman), Postdoc in Ecology & Evolutionary Biology
TITLE: "Decoding alarm signal propagation of seed-harvester ants, Pogonomyrmex californicus." ABSTRACT: Alarm signal propagation through social-insect colonies provides an empirically tractable context for analyzing information flow through a natural system, with useful insights for network dynamics in other social groups, including human social networks. Here, I develop a methodological approach to track alarm spread within the group of harvester ants, Pogonomyrmex californicus. I alarmed initial 3 individuals and tracked subsequent signal transmission through the group. Because there was no actual…
Find out more »Bioinformatics/Human Genetics Seminar Series: Erick Matsen, Professor, Public Health Sciences Division, Associate Program Head of Herbold Computational Biology Program, Fred Hutchinson Cancer Center
“Towards Bayesian phylogenetics via systematic search and gradient ascent” Hosted by Sriram Sankararaman
Find out more »QCBio Research Seminar: Chloe Yap, Visiting Graduate Student, University of Queensland
TITLE: "Restricted diet drives autism gut-microbiome associations, and other tales from the Australian Autism Biobank" ABSTRACT: The Australian Autism Biobank (AAB) is an initiative of the Autism CRC – the first national, cooperative research effort focused on autism across the lifespan. The AAB recruited a total of ~2,500 autistic children, family members, and unrelated undiagnosed children, and couples deep phenotypic information with multi-omic datasets (SNP genotyping, stool metagenomics, DNA methylation, metabolomics, WGS). One particularly controversial area in the field has…
Find out more »QCBio Research Seminar: Paheli Desai-Chowdhry (Savage), Grad student in Biomathematics
TITLE: "Asymmetric Branching Scale Factors as Features in Neuronal Cell-Type Classification" ABSTRACT: Neurons are connected by complex branching processes - axons and dendrites - that process information for organisms to respond to their environment. Classifying neurons according to differences in structure or function is a fundamental piece of neuroscience. In previous work, we constructed a biophysical theory that establishes a correspondence between neuron structure and function as mediated by principles such as time or power minimization, using undetermined Lagrange multipliers…
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