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Quantitative Biology Seminar Series

The qBio seminars will be from 1-2pm twice a month. Seminars are currently in-person at NSB 1205, but may occasionally be online.

The Zoom link will be sent in the email announcements.
If you would like to get announcements about qBio seminars, subscribe to the listserv below.
2023-24 Schedule
Date Speaker Affiliation Title

10/09/2023

Host: Lena Koslover

(recording)

Tzer Han Tan UCSD Chiral and Odd Dynamics in Living Matter

10/23/2023

Host: Mattia Serra

(recording)

Cristina Marchetti UCSB Rheology of Dense Biological Tissue

 

10/30/2023 Monthly qBio Student Presentations (12:30 PM in Bonner Hall 2130)

 

Haochen Fu (Suckjoon Jun Lab)

UCSD Physics Robust Control of DNA Replication Initiation in Escherichia Coli.

Maya Rowell (Stephanie Fraley Lab)

UCSD Bioengineering Development of a Fluidic Model System for Studying Cancer Vasculogenic Mimicry

11/06/2023

Host: Terry Hwa

(recording)

Urlich Gerland TU Munich Spatially Orchestrated Reaction Kinetics in Biological Systems

11/13/2023

Host: Tzer Han Tan

(recording)

 Saad Bhamla

GATech

The Blob: Topologically Entangled Living Matter

11/27/2023 Monthly qBio Student Presentations (12:30 PM in Bonner Hall 2130)

Shalni Kumar (Jeff Hasty Lab)

UCSD Bioengineeering

 

Exploiting Heterogeneity for Dynamic Microbial Population Adaptation

 

Livia Songster (Reck-Peterson Lab)

UCSD Biological Sciences The Role of Peroxisome Hitchhiking in Fungal Secondary Metabolism

12/04/2023

Host: Nigel Goldenfeld

(recording)

Will Ratcliff GATech Exploring the origin of multicellularity in real time: what we've learned from 5,000 generations of laboratory evolution

01/22/2024

 (recording)

Seugeun Oh UCSD Physics Exploring Pathophysiology via Single Cell Weight and BMI Analysis

01/29/2024 Monthly qBio Student Presentations (12:30 PM in Mayer Hall 4322)

Joe Solvason (Emma Farley Lab) UCSD Bioinformatics and Systems Biology Dissecting the Otx-a enhancer
Gabriel Mullin-Manzanarez (Terry Hwa Lab) UCSD Biological Sciences Proteome Remodeling and Survival in Starving Bacteria

02/05/2024

Host: Tzer Han Tan

(recording)

Suraj Shankar University of Michigan Wet, active solids: Physics and Physiology

02/26/2024

Host: Nigel Goldenfeld

Erwin Frey Ludwig Maximilian University of Munich Geometry in Motion: from protein patterns to cell-like function

03/11/2024

Host: Nigel Goldenfeld

TBA TBA TBA

04/1/2024

Host: Mattia Serra

Allon Klein Harvard TBA

04/15/2024

Host: Suckjoon Jun

Joshua Shaevitz Princeton TBA

04/29/2024

Host: Terry Hwa

Jan Skotheim Stanford TBA

05/13/2024

Host: Lena Koslover

Shankar Mukherji WashU TBA

06/03/2024

Host: Lena Koslover

Natalia Komarova UCSD Math TBA

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Seminar archive

2022-23

2022-23 Schedule
Date Speaker Affiliation Title

10/03/2022

Host: Terry Hwa

(recording)

Jing Yan Yale University Bacterial Biofilms as Shelf-Shaping Active Matter

10/17/2022

Host: David Kleinfled

Johnatan Aljadeff UCSD Neurobiology Shallow Networks Run Deep: How Peripheral Preprocessing Facilitates Odor Classification

 

10/24/2022 Monthly qBio Student Presentations (12:30 PM in MHA-2702)

 

Josh Borin (Justin Meyer Lab)

UCSD Biology Bacteria-Phage Coevolution Rapidly Drives the Emergence of Multi-Scale Networks 

Palka Puri (Yonathan Aljadeff Lab)

UCSD Physics Odor Processing by Specialized Interactions at the Olfactory Periphery 

10/31/2022

Host: Mattia Serra

(recording)

 

Alessandro Mongera Harvard Medical School, University College London Mechanical Regulation of Vertebrate Axis Elongation
11/21/2022 Monthly qBio Student Presentations (12:30 PM in MHA-2702)

Ximena Garcia Arceo (Brian Zid Lab)

UCSD Chemistry & Biochemistry Translation and Diffusion Kinetics Combine to Regulate mRNA Localization in Yeast

Xiang Ji (David Kleinfeld Lab)

UCSD Phyiscs Drawing and Analyzing the Plumbing Diagram of the Brain

01/09/2023

Host: Lena Koslover

Jun Allard UC Irvine Biophysics of T Cell Activation on Fluid Dynamic, Gene Regulatory, and Ultra-long Timescales

01/23/2023 Monthly qBio Student Presentations (12:30 PM in MHA-2702)

Granton Jindal UCSD Quantitative Biology of Developmental Abnormalities Caused by Mutations in the Ras/ERK Pathway
TBA TBA TBA

01/30/2023

Host: Suckjoon Jun

Achillefs Kapanidis University of Oxford Unraveling Transcription Mechanisms via Single-Molecule Imaging

02/13/2023

Host: Jack Reddan

(recording)

Corlett Wood University of Pennsylvania  The Conflict Between Your Feet: Interactions Between Mutualists and Parasites on the Same Host

02/27/2023

Host: Wouter-Jan Rappel

(recording)

Wallace Marshall UC San Francisco  How Cells Measure - the Flagellar Length Control System

03/13/2023

Host: Nigel Goldenfeld

(recording)

Orit Peleg University of Colorado, Boulder Physical Computation in Insect Swarms

04/10/2023

Host: Mattia Serra

(recording)

Boris Shraiman UC Santa Barbara Geometry and Mechanics in Epithelial Morphogenesis

04/17/2023 Monthly qBio Student Presentations (12:30 PM in the 7th Floor Urey Hall Coffee Area) 

Joe Solvason Emma Farley Lab Dissection of the Otx-a Enhancer
Pin-Chung Cheng  Kun Zhang Lab RETrace: Retrospective Single-cell Lineage Tracing with Microsatellites

04/24/2023

Host: Ghita Guessous

(recording)

Julia Schwartzman University of Southern California Collective Carbon Harvesting in Marine Bacteria

05/08/2023

Host: Lena Koslover

(recording)

Eleni Katifori University of Pennsylvania  Loops in Living Networks

05/15/2023 Monthly qBio Student Presentations (12:30 PM in Bonner Hall 2130

Sarah Ardell Kryazhimskiy Lab The Yeast Mutational Landscape Changes Predictably Across Strains and Environments
Tyler Goshia  Fraley Lab Development of a Rapid Cross-Kingdom Molecular Assay for Broad-Based Screening and Quantification of Viable Bacterial, Viral, and Fungal Pathogens

05/22/2023 on ZOOM at 10am PST

Host: Beverly Naigles

Kirsty Wan University of Exeter Physical and Embodied Intelligence at the Ciliate Surface

06/05/2023

Host: Suckjoon Jun

(recording)

John Glass JCVI Design, Construction, and Analysis of a Synthetic Minimal Bacterial Cell

2021-22

2021-22 Schedule
Date Speaker Affiliation Title

10/04/2021

Host: Terry Hwa

(recording)

Mattia Serra UC San Diego A Mechanochemical Model for Primitive Streak Formation Recapitulates Distinct Vertebrate Gastrulation Modes

10/18/2021

Host: Scott Rifkin

(recording

Michael Savageau UC Davis What Can Molecular Mechanisms Tell Us About The Distribution of Mutant Phenotypes and Their Evolution?

 

10/25/2021 Monthly qBio Student Presentations

Beverly Naigles (Hao Lab)

UCSD Biology Tracking the Dynamics of Immune Responses at a Single-Cell Level

Avaneesh Narla (Hwa Lab)

UCSD Physics How Do Populations Spread?

11/01/2021

Hosts: Sahana Kuthyar, Aspen Reese 

(recording)

Brandon Ogbunu Yale Using Protein Space to Explore Evolvability, Epistasis, and Druggability

11/15/2021

Host: Suckjoon Jun

(recording)

Jade Wang University of Wisconsin-Madison From 1940 to Present: What Bacteria Tell Us About the Mechanisms of Phenotypic and Genotypic Changes
11/22/2021 Monthly qBio Student Presentations Jacob Robertson (Hwa Lab) UCSD Biology Copiotroph’s delight: Growth and Aggregation of Alteromonas sp. 4B03 on Peptides and Amino Acids

Ryan Thiermann (Jun Lab)

UCSD Physics Do Bacterial Cells Allocate Resources to Maximize Growth?

11/29/2021

Hosts: Beverly Naigles, Terry Hwa

(recording)

Amy Schmid Duke University Gene Regulatory Networks Enable Resilience to Extreme Stress

01/10/2022

Hosts: Terry Hwa

(recording)

Robert Signer UC San Diego Hematopoietic Stem Cell Regulation by the Proteostasis Network

01/24/2022

Host: Lev Tsimring

(recording)

Lingchong You Duke University Antibiotic Response and Gene Transfer in Microbial Communities

02/07/2022

Host: Sergey Kryazhimskiy

(recording)

Kerry Geiler-Samerotte Arizona State University The Genotype - Phenotype - Phenotype - Phenotype Map

02/14/2022

Host: Terry Hwa

(recording)

Seppe Kuehn  University of Chicago The Structure-Function Problem in Microbial Communities

02/28/2022

Host: Todd Chou

(recording)

Dr. Markita del Carpio Landry UC Berkeley Nanomaterials Enable Delivery of Genetic Material Without Transgene Integration in Mature Plants

04/04/2022 

Host: Terry Hwa

Johannes Schoeneberg UC San Diego 4D Cell Biology: Adaptive Optics Lattice Light-Sheet Imaging and AI-Powered Big Data Processing of Live Stem Cell-Derived Organoids

04/11/2022 qBio Monthly Student Presentations

Tim Tyree (Rappel Lab) UC San Diego Cross-Modal Decoding of Individual Identity in the Primate Hippocampus
Shayna Holness (Hasty Lab) UC San Diego Protein Aggregation in the Context of Yeast Aging

05/02/2022

Hosts: Livia Songster, Sam Reck-Peterson

(recording)

Prachee Avasthi Dartmouth College

Mechanisms of Membrane Reorganization During Early Ciliary Growth 

05/09/2022

Host: Beverly Naigles

Rosie Alegado University of Hawaii - Manoa Resistance and Resilience Patterns of Subtropical Island Estuarine Microbial Assemblages in Response to Seasonal Forcing 

05/16/2022

Host: Gurol Suel

(recording)

Ido Golding University of Illinois-Urbana - Champaign Viral Decision Making: Some Recent Findings and Ongoing Work

05/23/2022 qBio Monthly Student Presentations

Saransh Umale (Jun Lab) UC San Diego TBA
Gabriel Manzanarez (Hwa Lab) UC San Diego TBA

2020-21

2020-21 Schedule
Date Speaker Affiliation Title

10/12/2020

(recording)

Kim Cooper UC San Diego

How (and why) the jerboa got its long feet

10/26/2020

(recording)

Michael Desai Harvard University Barcoded bulk QTL mapping in budding yeast

11/02/2020 Monthly qBio Student Presentations

(recording)

 

Alex Harvey    (Zid Lab)

UCSD Chem/Biochem

Translation Elongation Control During Stress in Yeast

Kaito Kakuchi (Suel Lab)

UCSD Biology

An Integrate-and-Fire Mechanism Drives Germination of Bacterial Spores

Fred Zhou (Sharpee Lab)

UCSD Biology

Hyperbolic Geometry of Olfactory Space

11/16/2020 (recording) Gaudenz Danuser
UT Southwestern Cell morphological control of oncogenic signals
11/23/2020 Vadim Gladyshev Harvard Medical School Quantifying and manipulating the aging process

11/30/2020

Monthly qBio Student Presentations

(recording)

Vinson Lam (Villa Lab)
UCSD Biology Circadian Chromosome Compaction in Cyanobacteria

Julie Roberts (Hao Lab)

UCSD Biology Sir2 Regulates Proteostasis During Aging

Nathan Palmer (Mali Lab) 

UCSD Biology Immune-Orthogonal AAV/Cas9 Combinations Circumvent the Immune Response to Gene Therapy
12/7/2020 Ming Chen Hammond University of Utah Discovering signaling enzymes through in vivo biochemistry experiments

1/11/2021

(recording)

Christine Jacobs-Wagner Stanford University Cell Size and Chromosome Folding: From Scaling Laws to Cellular Physicochemical Properties

1/25/2021

(recording)

Steph Weber McGill University No membrane, No problem: Condensing Bacterial Organelles
2/1/2021 Monthly qBio Student Presentations (recording)
Bijie Ren (Mayfield Lab) UCSD Biology Metabolic-Protein Secretion Modeling for Chlamydomonas Reinhardtii
Marco Man-Ho Tang (Rappel Lab) UCSD Physics Cellular Memory in Eukaryotic Chemotaxis Depends on the Background Chemoattractant Concentration
Anamika Agrawal (Koslover Lab)
UCSD Physics Optimizing Mitochondrial Maintenance in Neurons

2/22/2021

(recording)

Hunter Fraser Stanford University Using Hybrids to Explore the Evolution of Complex Traits

3/1/2021 Monthly qBio Student Presentations

(recording)

Tapan Goel (Shoetz-Collins Lab) UCSD Physics Non-Linear Elastodynamics of Hydra Mouth Opening
Matt Croxford (Villa Lab) UCSD Biology Compensating for Missing Wedge Artifacts in Cryo-Electron Tomography with Deconvolution
Chao Shi (Chao Lab) UCSD Biology Distribution of Gene Products in Bacteria Aging Landscape

3/8/2021

(recording)

Rachel Green Johns Hopkins University Ribosome Collisions Drive Cell Fate Decisions

4/5/2021

(recording)

Trent Northen Lawrence Berkeley National Lab Deconstructing the Role of Exudate Chemistry in Selecting Beneficial Rhizosphere Microbes

4/12/2021 Monthly qBio Student Presentations

(recording)

Huan-Yu Kuo (Kryzashimskiy Lab)
UCSD Physics Laboratory Experiment to Measure Random Mutations in Adaptive Evolution
Aravind Karanam (Rappel Lab) UCSD Physics Improved Chemotaxis through Repeated Stimulation

4/19/2021

(recording)

James O'Dwyer University of Illinois at Urbana-Champaign Resource Exchange, Stability and Coarse-Graining

5/3/2021

(recording)

Corina Tarnita Princeton University Self-organization and robustness in biological systems

5/10/2021 Monthly qBio Student Presentations

(recording)

Ghita Guessous (Hwa Lab)
UCSD Physics Chitin Degradation by Vibrio sp. 1A01
Jessica Bloom (Rifkin Lab) UCSD Biology Developmental System Drift in Caenorhabditis Nematodes and their Hybrids
5/17/2021 Allyson Sgro Boston University Connecting Intracellular Signaling Dynamics to Multicellular Decision Making

5/24/2021

(recording)

Dianne Newman Caltech Context Matters: Agathokakological Roles for Redox-Active "Antibiotics"

2019-20

2019-20 Schedule 
Date Speaker Affiliation Title

10/7/2019

Elena Koslover UC San Diego Navigating the maze: intracellular transport through organelle interactions and networks
10/21/2019 Arun Raj University of Pennsylvania Single cell analysis of therapy resistance in cancer
11/4/2019 Jian Liu
Johns Hopkins University Dividing up the genome: Do bacteria use a phase transition?
11/18/2019 Fitnat Yildiz UC Santa Cruz Mechanisms and Consequences of Biofilm Formation
12/2/2019 Vernita Gordon University of Texas, Austin Bacterial Mechanosensing: the Force will be with you, always
1/13/2020 Ethan Garner Harvard University How bacteria grow in defined rod shapes and control their rate of growth.
1/27/2020 Karmella Haynes Emory University Chromatin epigenetic engineering: combining synthetic biology with molecular bioinformatics.
2/10/2020 Rebecca Heald UC Berkeley Fun experiments you can only do with frogs
2/24/2020 Dan Fletcher UC Berkeley TBD
3/9/2020 Mike Rust University of Chicago Bayesian Modeling of the Cyanobacterial Clock
4/6/2020 Christine Jacobs-Wagner Stanford University Postponed due to COVID-19
5/4/2020 Michael Desai Harvard University Postponed due to COVID-19
5/18/2020 Corina Tarnita Princeton University Postponed due to COVID-19
6/1/2020 Rachel Green Johns Hopkins University Postponed due to COVID-19

2018-19

2018-19 Schedule
Date Speaker Affiliation Title
11/5/2018 Jianzhi Zhang University of Michigan Multi-environment fitness landscapes of a tRNA gene
11/26/2018 Diana Bautista UC Berkeley Itchy and scratchy: molecular mechanism of itch and pain
12/3/2018 Jeff Hasty UC San Diego Engineered gene circuits: From clocks to synchronized delivery
1/15/2019 Ning Jenny Jiang University of Texas, Austin High-throughput T cell repertoire profiling enabled systems immunology and immune engineering

1/28/2019 

Elaine Hsiao UCLA Host-microbiome interactions through the serotonergic system
2/25/2019 Michael Fischbach Stanford University Small molecules from the human microbiota
3/11/2019 Sean Brady Rockefeller University Watch your step, there is new chemistry everywhere
4/8/2019 Chunhui Chris Xu Cornell University Pushing the boundaries of multiphoton brain imaging
4/22/2019 Angela DePace Harvard University Precision and plasticity in animal transcription
5/6/2019 Sriram Kosuri UCLA Combining DNA synthesis, multiplexed reporters, and genome engineering to better understand human gene regulation and protein function
5/20/2019 Oleg Igoshin Rice University Pattern formation and multicellular self-organization behaviors in myxobacteria biofilms
6/3/2019 Brian Zid UC San Diego Factors impacting the localization and translation of nuclear-encoded mitochondrial mRNAs