Program

Welcome to the 2020 Bay Area RNA Club Meeting

Topics: Welcome Remarks, Conduct Reminder, Diversity Statement, Navigating Nooks

Keynote: The short and the long of cancer RNA sequencing

Angela Brooks, PhD | Oral presentation

Topics: nanopore sequencing, cancer, RNA splicing, RNA-Seq, alternative RNA splicing, Computational RNA splicing analysis

Dengue RNA-protein interactions that modulate infection in mosquito and human hosts

Shwetha Shivaprasad | Oral presentation

Topics: RNA virus, 3' untranslated region, RNA binding proteins, high-throughput assay

Dissecting Translation Start Site Selection in the Transcription Factor, CEBPA with CRISPRi

Sam Fernandez | Oral presentation

Topics: Translation control, translation initiation, uORFs, reinitiation, 5' untranslated region, CRISPR, CRISPRi

A developmental switch in RNA Polymerase III identity restricts transcription potential during cellular differentiation

Kevin Van Bortle, PhD | Oral presentation

Topics: gene regulation, gene expression, DNA-directed RNA polymerase, RNA polymerase, transcription, transcription factors, chromatin, exosome, tRNA

Revealing new molecular pathways for cancer cell fitness through a genetic screen of the cancer translatome

Duygu Kuzuoglu Ozturk, PhD | Oral presentation

Topics: Translation control, cancer, eIF4E, autophagy, EJC

Elongation Factor EF-G Enforces the Translational Reading Frame

Dustin Niblett | Oral presentation

Topics: Translation, ribosomal frameshifting, ribosomal translocation

SARS-CoV-2 disrupts protein synthesis in an unexpected way

Christopher Lapointe, PhD | Oral presentation

Topics: Translation control, ribosomes, SARS-CoV-2, translation initiation

Directed evolution of a ribosomal RNA methylating enzyme provides key insights into antibiotic resistance

Kaitlyn Tsai | Oral presentation

Topics: RNA modification, ribosomes, antibiotic resistance

Ribolog: an R package for unbiased analysis of ribosome profiling data

Hossein Asgharian, PhD | Oral presentation

Topics: Translation control, ribosome profiling, logistic regression, R package

Ligand-specific gene regulation in cobalamin riboswitches

Kristopher Kennedy | Oral presentation

Topics: Riboswitches, gene regulation, RNA structure, transcription, RNA ligand, microbiology

Statistical detection of regulated alternative splicing from single-cell RNA-seq data with the Splicing Z Score

Julia Olivieri, PhD | Oral presentation

Topics: single-cell genomics, bioinformatics, alternative RNA splicing

Full-Length Transcript Characterization for Single Cell RNA-seq Analysis

Elizabeth Tseng, PhD | Oral presentation

Topics: PacBio, single-cell genomics, isoforms, Iso-Seq, alternative RNA splicing, RNA sequencing

Structural Heterogeneity in Telomerase RNA

Nicholas Forino | Oral presentation

Topics: RNA structure, RNA folding, ribonucleoprotein

A roadmap of ribosome heterogeneity and its impact on cellular differentiation

Naomi Genuth | Oral presentation

Topics: ribosomes, ribosomal proteins, Translation control

Defining the breadth and specificity of drug response in heterogeneous immune cell populations using single-cell RNA sequencing

Chris McGinnis | Oral presentation

Topics: RNA sequencing, high-throughput assay, single-cell genomics, immunomodulation

Enabling real time analysis of massive single-cell datasets with accelerated computing and deep learning

Avantika Lal, PhD | Oral presentation

Topics: single-cell genomics, RNA sequencing, chromatin, epigenetics, machine learning, deep learning, accelerated computing, data visualization, bioinformatics, software

GAPLINC: Lnc-ing RNA and Inflammation in Macrophages

Apple Vollmers | Oral presentation

Topics: inflammation, lncRNA

In Vivo Genetic Interaction Screens of Driver Mutations Using Recombinase-Regulatable Synthetic CRISPR Arrays

Gabriel Eades, PhD | Oral presentation

Topics: CRISPR, GEMMs, Driver genes

RBMS1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon

Albertas Navickas, PhD | Oral presentation

Topics: RNA stability, colon cancer, metastasis

Careers in Industry I

Careers in Industry II

PhD to Postdoc I

PhD to Postdoc II

PhD to Postdoc III

Postdoc to PI I

Postdoc to PI II

Postdoc to PI III

A Strand Bias Assay to Detect Linear Extrachromosomal DNA (ecDNA)

William Wang | ePoster

Topics: Computational Biology, Extrachromosomal DNA, DNA Sequencing

A structured viral RNA uses molecular mimicry and conformational dynamics to coordinate multiple functions

Jeffrey Kieft, PhD | ePoster

Topics: RNA structure, viral RNA, tRNA, cryo-electron microscopy, RNA dynamics

Analysis of ARM-seq and DM-tRNA-seq using tRAX allows for detection of tissue-specific tRNA/tDRNA expression and modifications

Jonathan Howard, PhD | ePoster

Topics: tRNA, tRNA molecules, tRNA-derived fragment, tRNA pools, tRNA gene function, high-throughput assay, RNA sequencing, Base modifications, RNA modification, Small cytoplasmic RNA

Analysis of mRNP Complexes by Fluorescence Correlation and Cross-Correlation Spectroscopy

Àngels Mateu-Regué | ePoster

Topics: messenger RNA mRNA, mRNA localization, ribonucleoprotein, RNA binding proteins, RNA dynamics, single molecule analysis, Fluorescence Correlation Spectroscopy, Fluorescence Microscopy

Chemically modified antisense guide oligonucleotides for Adenosine Deaminases acting on RNA (ADAR) editing of a Rett Syndrome target

Hannah Brinkman | ePoster

Topics: RNA editing, Double-stranded RNA

CRISPRi-based genetic screen of functional long non-coding RNAs in Ewing Sarcoma

Marcela Briones, PhD | ePoster

Topics: CRISPRi, lncRNA, screening

Detection of Alternative Isoforms of Gene Fusions Using Long-Read Nanopore RNA-seq

Colette Felton | ePoster

Topics: Computational RNA splicing analysis, RNA splicing, isoforms, data visualization, Driver genes, RNA technology

Diversity of RNA structures replicated by T7 DNA dependent RNA polymerase (DdRP)

Amisha Kumar | ePoster

Topics: RNA structure, RNA amplification, Computational Biology

Functional characterization of the RNA interference machinery of Aspergillus fumigatus

Abdulrahman Kelani, MD | ePoster

Topics: RNA interefrence, Small interfering RNA, gene regulation

Gammaherpesviruses alter the tRNA expression landscape

Jessica Tucker, PhD | ePoster

Topics: gammaherpesvirus, tRNA, tRNA-derived fragment, gene expression

Influence of circular target RNA topology on miRNA stability and function

Federico Fuchs Wightman | ePoster

Topics: microRNA, circRNA, TDMD

MESA: A Tool for Comprehensive Splicing Quantification

Dennis Mulligan | ePoster

Topics: Computational RNA splicing analysis, alternative RNA splicing

Mitochondrial function governs Smaug MLO dissolution

Graciela Boccaccio, PhD | ePoster

Topics: membraneless organelles, ribonucleoprotein, Liquid-liquid phase separation

Nucleotide-resolution Assessment of tRNAs and tRNA-derived small RNAs Across Mouse Tissues

Aidan Manning, PhD | ePoster

Topics: tRNA, tRNA-derived fragment, tRNA molecules, tRNA pools

One transcript, distinct stabilities: The methionine biosynthesis operon in Staphylococcus aureus

Freya Wencker, PhD | ePoster

Topics: Riboswitches, T-box Riboswitch, 5' untranslated region, RNA decay, RNA stability, Staphylococcus aureus

Polyspecific CRISPR approaches to unlock combination based therapies

Stefan Oberlin | ePoster

Topics: CRISPR, cancer, gene regulation

Post-transcriptional regulation of a developmental EMT program is mediated by P-bodies

Erica Hutchins, PhD | ePoster

Topics: RNA decay, post-transcriptional RNA processing, embryo development

Spatial mapping of diverse gene signatures and cell type specific markers across mouse brain using the RNAscope™ HiPlexUp in situ hybridization assay.

Jyoti Sheldon | ePoster

Topics: RNAscope, HiPlex, Single cell, RNA, Neuroscience

Spatial profiling of highly homologous 3R and 4R Tau isoforms during mouse brain development using BaseScopeTM in situ hybridization technology

Jyoti Sheldon | ePoster

Topics: Tau, RNAscope, Spatial Biology, in situ hybridization, neurodegenerative diseases

Step into the Unresolved: Versatile Tools Towards Real-time Single-molecule Biology

Nastaran Hadizadeh, PhD | ePoster

Topics: RNA structure, RNA binding proteins, RNA polymerase

Understanding the contribution of somatic mutations in the splicing factor U2AF1 in the context of other driver mutations in lung cancer.

eva robinson, PhD | ePoster

Topics: alternative RNA splicing, cancer, RNA sequencing

High-resolution view of HIV-1 Reverse Transcriptase initiation and its inhibition by NNRTI drugs

Betty Ha | ePoster

Topics: HIV-1, viral replication, RNA, protein, Reverse Transcriptase, cryo-EM

An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans

Lamia Wahba, PhD | ePoster

Topics: Small interfering RNA, ribosomal RNA

Characterization of tRNAs and tRNA-derived Small RNAs in Human Cerebral Cortical Organoids

Alex Bagi | ePoster

Topics: tRNA, transfer RNA, tRNA-derived fragment, neurodevelopment

Decoding the Mechanistic Principles of Gene Regulation by Mitochondrial 3D Spatial Organization

Tatsuhisa Tsuboi, PhD | ePoster

Topics: messenger RNA mRNA, mRNA localization, mitochondria

Engineering the retron reverse transcriptase to produce customizable ssDNA as a tool for synthetic biology

Christina Palka, PhD | ePoster

Topics: Reverse Transcriptase, RNA structure, bioinformatics, Synthetic biology

Establishment of a stoichiometry analysis method for characterizing mRNP composition by single molecule TIRF imaging

Ryuta Asada, PhD | ePoster

Topics: mRNP, mRNA export, single molecule analysis

eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants

Alexis Thornton | ePoster

Topics: gene expression, cancer, RNA sequencing, bioinformatics

Health and Disease Across Generations: Identification of endonucleases involved in the cleavage of Transfer RNA's in the male reproductive tract

Elvira Antonia Contreras | ePoster

Topics: enzymes cleaving RNA, epigenetics, endonucleases, tRNA molecules, tRFs, sperm, environmental conditions, family A endonucleases, family T2 endonucleases, Rnases 9, embryo development, ribonuclease(s), reproductive tract, stress, cancer, neurodegenerative disease, obesity, diabetes, healthy living, behavioral research

Mechanism of transcriptional silencing by piRNAs

Maria Ninova, PhD | ePoster

Topics: piRNAs, chromatin, epigenetics, silencing, transposons, SUMO

Mechanisms of Conserved RNA localization

Raeann Goering | ePoster

Topics: mRNA localization, ribonucleoprotein

Nucleotide resolution profiling of m3C RNA modification by HAC-seq

Jia Cui, PhD | ePoster

Topics: RNA modification, RNA sequencing

Pan-cancer, pervasive upregulation of 3’UTR splicing drives tumorigenesis

Yvonne Tay, PhD | ePoster

Topics: alternative polyadenylation, RNA splicing, 3' untranslated region, cancer

Potential tRNAs interfering with Pol2 transcription: VAC14

Qiuxia Tang, MD, PhD | ePoster

Topics: tRNA, tRNA gene function

RNA binding protein IGF2BP1/IMP1 regulates translation of autophagy pathway genes

Patrick Williams, PhD | ePoster

Topics: RNA binding proteins, intestinal epithelium

SARS-CoV2 novel transcript detection with SICILIAN identifies known and novel discontinuous splicing events

Rob Bierman | ePoster

Topics: SARS-CoV-2, transcription, Computational RNA splicing analysis

Single molecule dynamics of eIF4F-mediated mRNA cap recognition

Burak Cetin | ePoster

Topics: translation initiation

Spatially-resolved high-plex in situ RNA expression profiling with NanoString GeoMx Whole Transcriptome Atlas

Eugene Cilento, PhD | ePoster

Topics: RNAseq, RNAscope, scRNAseq, Spatial Biology, Whole Transcriptome, cancer, FFPE

Statistical detection of splice sites that drive differential alternative splicing in single cells

Roozbeh Dehghannasiri, PhD | ePoster

Topics: single-cell genomics, alternative RNA splicing, Computational RNA splicing analysis

Structure of the SARS-CoV-2 Nsp1/5′-Untranslated Region Complex and Implications for Potential Therapeutic Targets, a Vaccine, and Virulence

Naveen Vankadari, PhD | ePoster

Topics: RNA binding proteins, ribosomes, RNA virus, 5' untranslated region, gene expression, ribosomal translocation

Systematic Characterization of Branchsite Mutations Perturbing RNA Splicing

Yi-Ting Chen | ePoster

Topics: alternative RNA splicing, Intron, Branch site, Computational RNA splicing analysis

TDP-43 and HSP70 phase separate into anisotropic, intranuclear liquid spherical shells

Haiyang Yu, PhD | ePoster

Topics: Liquid-liquid phase separation, ribonucleoprotein

The genomic Z score (GZS) detects changes in mRNA processing in single-cell data

Elisabeth Meyer | ePoster

Topics: single-cell genomics, alternative RNA splicing, alternative polyadenylation

Using CRISPR/Cas9 to Identify Oncogenic Splicing Events in Lung Adenocarcinoma

Megan Durham | ePoster

Topics: RNA splicing, CRISPR

A microRNA linking human positive selection and metabolic disorders

Anders Naar, PhD | ePoster

Topics: microRNA, Metabolism

A moonlighting microRNA: human miR-122-mediated viral RNA accumulation and mechanism(s) of resistance to miR-122-based therapies

Selena Sagan, PhD | ePoster

Topics: RNA structure

A rare codon-based translational program of cell proliferation

Joao Guimaraes, PhD | ePoster

Topics: Cell proliferation, Translation control, Codon usage, Rare codons, Translation elongation, tRNA pools

A small RNA-mediated feedback loop maintains proper levels of 22G-RNAs in C. elegans

Alicia Rogers, PhD | ePoster

Topics: gene regulation, Small interfering RNA, RNA amplification

A T1D-associated lncRNA modulates the type I interferon signaling and the antiviral response in pancreatic beta cells.

itziar gonzalez | ePoster

Topics: type 1 diabetes, iDIN, lncRNA, pancreatic beta cell, SNP

Applications of ribosome profiling (RIBO-seq) for high-resolution analysis of protein expression at proteome level.

Silvia Tornaletti, PhD | ePoster

Topics: translation regulation, ribosome profiling

Characterization of piRNA populations

Daniel Stoyko | ePoster

Topics: Piwi RNA, RNA sequencing

Comprehensive sequence-to-function mapping of ligand-dependent RNA catalysis

Andrew Savinov, PhD | ePoster

Topics: Riboswitches, ribozymes, RNA array, high-throughput assay, gene regulation

Exploring the piRNA sequence space and the potential of piRNA-mediated silencing.

Parthena Konstantinidou | ePoster

Topics: piRNA

Functional implications of PIWI-interacting RNA (piRNA) diversity and abundance.

Pavol Genzor, PhD | ePoster

Topics: Piwi RNA, silencing, ribonucleoprotein

Gluten-induced RNA methylation changes regulate intestinal inflammation via allele-specific XPO1 translation in epithelial cells

Ane Olazagoitia-Garmendia | ePoster

Topics: SNP, m6a, 5' UTR, NFkB, inflammation, gluten, celiac disease CD

Identifying a functional exosomal circLPAR1 as early diagnostic biomarkers of colorectal cancer

Mulong Du, MD, PhD | ePoster

Topics: exosome, circRNA, colorectal cancer, biomarker

Interplay between miRNA precursors and biogenesis enzymes promotes a widespread increase of aberrant isoforms in tumors

Xavier Bofill De Ros, PhD | ePoster

Topics: microRNA, cancer, Drosha, Dicer1, biogenesis, isoforms

Interrogating the role of ADAR1 in lung adenocarcinoma through identification of A-to-I editing in long reads

Alison Tang, PhD | ePoster

Topics: RNA editing, cancer, nanopore sequencing

LABRAT reveals association of alternative polyadenylation with transcript localization, RBP expression, transcription speed, and cancer survival

Matthew Taliaferro, PhD | ePoster

Topics: alternative polyadenylation, cancer, gene expression

METTL1-mediated m7G tRNA modification drives oncogenic transformation

Esteban Orellana, PhD | ePoster

Topics: RNA modification, cancer, Translation

Oncogenic circFAM120A promotes cognate mRNA translation in an IGF2BP2 dependent manner

Xiang Li, PhD | ePoster

Topics: Functional circRNA screening, Translation control, Cell proliferation

RNA editing plays a primary role in common autoimmune diseases

Qin Li, PhD | ePoster

Topics: RNA editing, Genetic Variation, Double-stranded RNA

Screening for functional circular RNAs using the CRISPR-Cas13 system

Siqi Li, PhD | ePoster

Topics: Functional circRNA screening

Site-Selective RNA Modification via DNA-induced Structure

Lu Xiao, PhD | ePoster

Topics: RNA modification

The short and long-range RNA-RNA Interactome of SARS-CoV-2

Omer Ziv, PhD | ePoster

Topics: RNA structure, RNA technology, RNA virus

Transcription polymerase–catalyzed emergence of novel RNA replicons

Nimit Jain | ePoster

Topics: RNA amplification, RNA genomics, transcription

tRNAArg-Derived Fragments Can Serve as Arginine Donors for Protein Arginylation

Irem Avcilar-Kucukgoze, PhD | ePoster

Topics: transfer RNA, tRNA-derived fragment, arginylation