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.
| Date | Speaker | Affiliation | Title |
10/09/2023Host: Lena Koslover |
Tzer Han Tan | UCSD | Chiral and Odd Dynamics in Living Matter |
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10/23/2023 Host: Mattia Serra |
Cristina Marchetti | UCSB | Rheology of Dense Biological Tissue |
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10/30/2023 Monthly qBio Student Presentations (12:30 PM in Bonner Hall 2130)
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Haochen Fu (Suckjoon Jun Lab) |
UCSD Physics | Robust Control of DNA Replication Initiation in Escherichia Coli. |
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Maya Rowell (Stephanie Fraley Lab) |
UCSD Bioengineering | Development of a Fluidic Model System for Studying Cancer Vasculogenic Mimicry | |
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11/06/2023 Host: Terry Hwa |
Urlich Gerland | TU Munich | Spatially Orchestrated Reaction Kinetics in Biological Systems |
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11/13/2023 Host: Tzer Han Tan |
GATech |
The Blob: Topologically Entangled Living Matter |
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| 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
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Livia Songster (Reck-Peterson Lab) |
UCSD Biological Sciences | The Role of Peroxisome Hitchhiking in Fungal Secondary Metabolism | |
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12/04/2023 Host: Nigel Goldenfeld |
Will Ratcliff | GATech | Exploring the origin of multicellularity in real time: what we've learned from 5,000 generations of laboratory evolution |
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01/22/2024 |
Seugeun Oh | UCSD Physics | Exploring Pathophysiology via Single Cell Weight and BMI Analysis |
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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 | |
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02/05/2024 Host: Tzer Han Tan |
Suraj Shankar | University of Michigan | Wet, active solids: Physics and Physiology |
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02/26/2024 Host: Nigel Goldenfeld |
Erwin Frey | Ludwig Maximilian University of Munich | Geometry in Motion: from protein patterns to cell-like function |
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03/11/2024 |
Elizabeth Villa | UCSD Department of Molecular Biology |
Opening Windows into the Cell: Bringing Structure to Cell Biology using in-cellulo cryo-Electron Microscopy
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04/1/2024 Host: Mattia Serra |
Allon Klein | Harvard Medical School | Learning dynamics from single cell snapshots: lessons from physics |
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04/15/2024 Host: Suckjoon Jun
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Joshua Shaevitz | Princeton | Magic or mechanics? Understanding dynamics in living systems |
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04/22/2024 Monthly qBio Student Presentations (12:30 PM in Mayer Hall 4322) |
Sahana Kuthyar (Allen Lab) | UCSD Biological Sciences | Microbiome-mediated resistance is shaped by invader identity and host domestication status |
| Todd Chou (Süel Lab) | UCSD Biological Sciences | A segmentation clock patterns cellular differentiation in a bacterial biofilm | |
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04/29/2024 Host: Terry Hwa |
Jan Skotheim | Stanford | Cell Size Control |
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05/13/2024 Host: Lena Koslover |
Shankar Mukherji | WashU | Building the cell from unreliable parts: coordinating stochastic organelle biogenesis with cellular growth |
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05/20/2024 Monthly qBio Student Presentations (12:30 PM in Bonner Hall 2130) |
Sreejith Santhosh (Mattia Serra Lab) | UCSD Physics | Patterning mechanisms in pre-gastrulation chick embryo |
| Camilo Rey-bedon (Hasty Lab) | UCSD Biological Sciences | A Micro-physiological Window to Explore Bacterial Therapeutics in the Tumor Microenvironment | |
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06/03/2024 Host: Lena Koslover |
Natalia Komarova | UCSD Math | Mathematical Methods in Evolution and Medicine |
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Seminar archive
2022-23
| Date | Speaker | Affiliation | Title |
10/03/2022Host: Terry Hwa |
Jing Yan | Yale University | Bacterial Biofilms as Shelf-Shaping Active Matter |
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10/17/2022 Host: David Kleinfled |
Johnatan Aljadeff | UCSD Neurobiology | Shallow Networks Run Deep: How Peripheral Preprocessing Facilitates Odor Classification |
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10/24/2022 Monthly qBio Student Presentations (12:30 PM in MHA-2702)
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Josh Borin (Justin Meyer Lab) |
UCSD Biology | Bacteria-Phage Coevolution Rapidly Drives the Emergence of Multi-Scale Networks |
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Palka Puri (Yonathan Aljadeff Lab) |
UCSD Physics | Odor Processing by Specialized Interactions at the Olfactory Periphery | |
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10/31/2022 Host: Mattia Serra
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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 |
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Xiang Ji (David Kleinfeld Lab) |
UCSD Phyiscs | Drawing and Analyzing the Plumbing Diagram of the Brain | |
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01/09/2023 Host: Lena Koslover |
Jun Allard | UC Irvine | Biophysics of T Cell Activation on Fluid Dynamic, Gene Regulatory, and Ultra-long Timescales |
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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 | |
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01/30/2023 Host: Suckjoon Jun |
Achillefs Kapanidis | University of Oxford | Unraveling Transcription Mechanisms via Single-Molecule Imaging |
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02/13/2023 Host: Jack Reddan |
Corlett Wood | University of Pennsylvania | The Conflict Between Your Feet: Interactions Between Mutualists and Parasites on the Same Host |
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02/27/2023 Host: Wouter-Jan Rappel |
Wallace Marshall | UC San Francisco | How Cells Measure - the Flagellar Length Control System |
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03/13/2023 Host: Nigel Goldenfeld |
Orit Peleg | University of Colorado, Boulder | Physical Computation in Insect Swarms |
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04/10/2023 Host: Mattia Serra |
Boris Shraiman | UC Santa Barbara | Geometry and Mechanics in Epithelial Morphogenesis |
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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 |
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04/24/2023 Host: Ghita Guessous |
Julia Schwartzman | University of Southern California | Collective Carbon Harvesting in Marine Bacteria |
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05/08/2023 Host: Lena Koslover |
Eleni Katifori | University of Pennsylvania | Loops in Living Networks |
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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 | |
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05/22/2023 on ZOOM at 10am PST Host: Beverly Naigles |
Kirsty Wan | University of Exeter | Physical and Embodied Intelligence at the Ciliate Surface |
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06/05/2023 Host: Suckjoon Jun |
John Glass | JCVI | Design, Construction, and Analysis of a Synthetic Minimal Bacterial Cell |
2021-22
| Date | Speaker | Affiliation | Title |
10/04/2021Host: Terry Hwa |
Mattia Serra | UC San Diego | A Mechanochemical Model for Primitive Streak Formation Recapitulates Distinct Vertebrate Gastrulation Modes |
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10/18/2021 Host: Scott Rifkin |
Michael Savageau | UC Davis | What Can Molecular Mechanisms Tell Us About The Distribution of Mutant Phenotypes and Their Evolution? |
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10/25/2021 Monthly qBio Student Presentations |
Beverly Naigles (Hao Lab) |
UCSD Biology | Tracking the Dynamics of Immune Responses at a Single-Cell Level |
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Avaneesh Narla (Hwa Lab) |
UCSD Physics | How Do Populations Spread? | |
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11/01/2021 Hosts: Sahana Kuthyar, Aspen Reese |
Brandon Ogbunu | Yale | Using Protein Space to Explore Evolvability, Epistasis, and Druggability |
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11/15/2021 Host: Suckjoon Jun |
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 |
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Ryan Thiermann (Jun Lab) |
UCSD Physics | Do Bacterial Cells Allocate Resources to Maximize Growth? | |
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11/29/2021 Hosts: Beverly Naigles, Terry Hwa |
Amy Schmid | Duke University | Gene Regulatory Networks Enable Resilience to Extreme Stress |
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01/10/2022 Hosts: Terry Hwa |
Robert Signer | UC San Diego | Hematopoietic Stem Cell Regulation by the Proteostasis Network |
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01/24/2022 Host: Lev Tsimring |
Lingchong You | Duke University | Antibiotic Response and Gene Transfer in Microbial Communities |
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02/07/2022 Host: Sergey Kryazhimskiy |
Kerry Geiler-Samerotte | Arizona State University | The Genotype - Phenotype - Phenotype - Phenotype Map |
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02/14/2022 Host: Terry Hwa |
Seppe Kuehn | University of Chicago | The Structure-Function Problem in Microbial Communities |
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02/28/2022 Host: Todd Chou |
Dr. Markita del Carpio Landry | UC Berkeley | Nanomaterials Enable Delivery of Genetic Material Without Transgene Integration in Mature Plants |
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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 |
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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 | |
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05/02/2022 Hosts: Livia Songster, Sam Reck-Peterson |
Prachee Avasthi | Dartmouth College |
Mechanisms of Membrane Reorganization During Early Ciliary Growth |
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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 |
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05/16/2022 Host: Gurol Suel |
Ido Golding | University of Illinois-Urbana - Champaign | Viral Decision Making: Some Recent Findings and Ongoing Work |
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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
| Date | Speaker | Affiliation | Title |
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10/12/2020 |
Kim Cooper | UC San Diego |
How (and why) the jerboa got its long feet |
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10/26/2020 |
Michael Desai | Harvard University | Barcoded bulk QTL mapping in budding yeast |
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11/02/2020 Monthly qBio Student Presentations
|
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 |
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| Fred Zhou (Sharpee Lab) |
UCSD Biology |
Hyperbolic Geometry of Olfactory Space |
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| 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 |
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11/30/2020 Monthly qBio Student Presentations |
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 |
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1/11/2021 |
Christine Jacobs-Wagner | Stanford University | Cell Size and Chromosome Folding: From Scaling Laws to Cellular Physicochemical Properties |
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1/25/2021 |
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 |
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2/22/2021 |
Hunter Fraser | Stanford University | Using Hybrids to Explore the Evolution of Complex Traits |
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3/1/2021 Monthly qBio Student Presentations |
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 | |
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3/8/2021 |
Rachel Green | Johns Hopkins University | Ribosome Collisions Drive Cell Fate Decisions |
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4/5/2021 |
Trent Northen | Lawrence Berkeley National Lab | Deconstructing the Role of Exudate Chemistry in Selecting Beneficial Rhizosphere Microbes |
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4/12/2021 Monthly qBio Student Presentations |
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 | |
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4/19/2021 |
James O'Dwyer | University of Illinois at Urbana-Champaign | Resource Exchange, Stability and Coarse-Graining |
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5/3/2021 |
Corina Tarnita | Princeton University | Self-organization and robustness in biological systems |
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5/10/2021 Monthly qBio Student Presentations |
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 |
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5/24/2021 |
Dianne Newman | Caltech | Context Matters: Agathokakological Roles for Redox-Active "Antibiotics" |
2019-20
| 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
| 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 |
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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 |
