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InSiDE Seminar Series

Insights in Signaling Dynamics and Encoding is a weekly online seminar series featuring PIs, postdocs, and students. The 2022 series starts June 9th! Come join us to hear about cutting edge research.


Our Mission is to bring together scientists with a shared interest in single-cell signaling dynamics, to provide a venue to present and share cutting edge research, and to foster a global community of diverse and talented scientists at all levels of training.

ERK waves in MDCK cells, visualized with EKAR-EV
(copyright Olivier Pertz)



Single-cell analysis

There is a surprising degree of heterogeneity within populations of cells, even between genetically identical cells. Only by measuring single-cells can this heterogeneity be captured.

Dynamic measurements

Signaling processes are highly dynamic, even under steady-state conditions, and cells often encode information within these signaling dynamics. Advances in time-lapse imaging, fluorescent biosensors, and image analysis pipelines have made it possible to de-code this information.

Mathematical models

Signaling circuits are highly complex. Computational models can be used not only to describe signaling events, but also to understand why these events occur.

Latest News:

September 1
Speaker 1: Gregor Neuert, PhD (Associate Professor, Vanderbilt University)
“Determining mechanisms of regulation by antisense long noncoding RNAs”

Speaker 2: Matthias Heinemann, PhD (Professor, University of Groningen)
“Metabolic dynamics during the cell cycle”


August 25
Speaker 1: Debasish Paul, PhD (Postdoc, Cappell lab, NCI)
“An mTOR-APC/C-phosphatase loop mediates a metabolic switch during cell-cycle entry”

Speaker 2: Lucas Pelkmans, PhD (Professor, University of Zurich) 
“Multimodal perception links cellular state to decision making in single cells”


August 18
Speaker 1: Nick DeCuzzi (Graduate student, Albeck lab, UC Davis)
“Lung Epithelial Micro-Environment Modulates Spatial ERK Signaling Dynamics” 

Speaker 2: Jen Oyler-Yaniv, Phd (Principal Investigator, Harvard Medical School)
“Plasticity in cell fate during infection shapes the inflammatory response”


August 11
Speaker 1: Michelle Frei, PhD (Postdoc, Zhang lab, UC San Diego)
“A new dimension: HaloTag variants for fluorescence lifetime multiplexing”

Speaker 2: David Suter, PhD (Associate Professor, EPFL)
“Dynamics of H2A.Z through the cell cycle”


August 4
Speaker 1: Stefan Lundgren (Graduate student, Collins lab, UC Davis)
“Signaling dynamics distinguish high and low priority neutrophil attractant receptors”

Speaker 2: Ran Kafri, PhD (Assistant Professor, University of Toronto) 


July 28
Speaker 1: Shah Md Toufiqur Rahman, PhD (Postdoc, Sung Lab, NIA)
“NF-κB reporter mouse models: a new tool for monitoring endogenous NF-κB activity at single-cell resolution”

Speaker 2: Davide Mazza, PhD (Associate Professor, San Raffaele Scientific Institute)
“Single molecule tracking to probe the transcription factor search mechanism in eukaryotes”


July 21
Speaker 1: Humza Ashraf (Graduate Student, Spencer Lab, UC Boulder)
“Beta-galactosidase marks long durations of cell cycle exit rather than exclusively cellular senescence”

Speaker 2: Josh Leonard, PhD (Associate Professor, Northwestern University)
“Probing and programming mammalian gene expression programs using synthetic biology”


July 14
Speaker 1: Devan Murphy (Graduate Student, Albeck Lab, UC Davis)
“Combinatorial signaling dynamics of NF-kB, ERK, and AMPK that regulate IL-8”

Speaker 2: Rachel Gottschalk, PhD (Assistant Professor, University of Pittsburgh)
“Computational modeling of STAT activation features that predict gene expression profiles”


July 7
Speaker 1: Timm Schroeder, PhD (Professor, ETH Zurich)
“Long-term single-cell dynamics quantification: New tools for old questions”

Speaker 2: Tobias Kull, PhD (Postdoc, Schroeder Lab, ETH Zurich)
“NF-κB signaling dynamics throughout the hematopoietic system”


June 30th
Speaker 1: Marwa Afifi, PhD (Postdoc, Cappell Lab, NCI)
“MYC inactivation is necessary for the commitment to and maintenance of cellular senescence”

Speaker 2: Carla Mulas, PhD (King’s Prize Fellow, King’s College London)
“Signalling dynamics during cell state transitions”


June 23rd
Speaker 1: Beverly Naigles (Graduate Student, Hao Lab, UC San Diego)
“Tracking the dynamics of immune responses at a single-cell level”

Speaker 2: Veronica Biga, PhD (Research Fellow, Papalopulu Lab, University of Manchester)
“Multiscale, dynamic and spatially-periodic coordination of gene expression in spinal cord progenitor cells”


Our 2022 seminar series kicks off June 9! We will have two excellent keynote speakers in back-to-back weeks. Following the keynote on June 16, we will have a virtual poster session to jumpstart this years InSiDE talks.
Come join us!

June 9: Keynote: Dr. Shinya Kuroda, University of Tokyo
“Systems Biology of Insulin Action and Metabolism”

(*note special start time of 23 GMT/7pm EDT/4pm PDT)

June 16: Keynote: Dr. Hana El-Samad, Altos Labs
“Respect the loops”

(Seminar begins at 15:30 GMT/11:30am EDT/8:30am PDT)
Following the seminar, there will be an online poster session on gather.town at 16:30 GMT
Click Here to register to present a poster. Registration closes June 10.


Virtual Poster Session, June 16
16:30 GMT/12:30pm EDT/9:30am PDT

Register to present a poster by June 1:


May 19, 2022
Workshop: Analysis of single-cell time series data

  • Using a pipeline to import, pre-process and extract parameters from single-cell time series data
  • Time series decomposition and Principal Components Analysis
  • Correlating live-cell activity with gene expression
  • Oscillatory signals and wavelet analysis
  • Discussion time: Bring your hardest data analysis questions!!

Workshop leaders:
Mathias Heltberg (Niels Bohr Institute)
Michael Pargett (University of California, Davis)
Adrian Granada (Charité Comprehensive Cancer Center, Berlin)

15:30 GMT/11:30am EDT/8:30am PDT


April 21, 2022
Workshop: Long-term imaging and quantification of mRNAs in live single cells using SunRISER and dNEMO

This workshop will provide an overview of how to implement the SunRISER approach for live-cell imaging of single mRNAs and a demonstration for rapid automated and semi-automated detection of fluorescent puncta from time-lapse images using the dNEMO interface.

Workshop leaders:
Gabriel Kowalczyk (Lee Lab, University of Pittsburgh)
Yue Guo (Lee Lab, University of Pittsburgh)
Zachary Hemminger (Wollman Lab, UCLA)

16:30 GMT/11:30am EDT/8:30am PDT


March 10, 2022
Optogenetics workshop: from the fundamentals to the cutting edge. 

Learn how to construct your own optogenetic tools for the modulation of intracellular signaling, how to use a simple LED-device for precise temporal activation, and how to set up a platform for single-cell feedback-control experiments.

Workshop leaders:
Lucien Hinderling, University of Bern
Thomas Hӧhener, University of Bern
Lorena Benedetti, Janelia Research Campus

16:30 GMT/11:30am EST/8:30am PST


That Concludes the 2021 InSiDE Seminar Series. Join us next summer for another slate of talks on signaling dynamics!


October 14th
Speaker 1: Jennifer Klomp, PhD (Postdoc, Der lab, UNC Chapel Hill)
“ERK finds a way: targeting ERK-MAPK in KRAS mutant PDAC”

Speaker 2: Mia Sung, PhD (Stadtman Investigator, National Institute of Aging)
“Imaging endogenous NF-kB dynamics to study cell-specific signal encoding”


October 7th
Speaker 1: Jordan Fauser (Graduate Student, Karginov Lab, University of Illinois Chicago)
“Dissecting Shp2 phosphatase signaling through engineered allosteric control”

Speaker 2: Pawel Paszek, PhD (Senior Lecturer, The University of Manchester)
“Regulation of cellular variability in the immune system”


September 30th
Speaker 1: Kathleen Lasick (Graduate Student, Paek Lab, University of Arizona)
“Stimulus-dependent dynamics of the Foxo1 transcription factor”

Speaker 2: Lukasz Bugaj, PhD (Assistant Professor, University of Pennsylvania)
“Altered signal perception and drug tolerance via oncogenic protein aggregates”


September 23rd:
Speaker 1: Laura Friedel, MSc (Graduate student, Loewer Lab, TU Darmstadt)
“From acute to persisting damage: CHK2 is crucial for sustaining the p53 response”

Speaker 2: Marc Birtwistle (Associate Professor, Clemson University)
“Predicting individual cell division events from single-cell ERK and Akt dynamics”


September 16th:
Speaker 1: Kiran Vanaja, PhD (Associate Research Scientist, Levchenko Lab, Yale University)
“Computation modeling helps reveal PTEN as a negative feedback loop of the PI3K/Akt/mTOR signaling pathway”

Speaker 2: Laura Heiser, PhD (Associate Professor, Oregon Health Science University)
“A systems biology approach to dissect complex cellular phenotypes”


September 9th:
Speaker 1: Lindsey Osimiri (Graduate student, El-Samad Lab, UCSF)
“Optogenetic control of RelA translocation reveals differential gene induction”

Speaker 2: Mounia Lagha, PhD (Group Leader, Institute de Génétique Moléculaire de Montpellier)


September 2nd:
Speaker 1: Stefanie Luecke, PhD (Postdoc, Hoffman Lab, UCLA)
“Combinatorial and temporal signaling codes controlling immune responses by macrophages”

Speaker 2: Brian Munsky, PhD (Associate Professor, Colorado State University)
“Measuring, modeling, and predicting the central dogma at single-gene and single-mRNA resolution”


August 26th:
Speaker 1: Julie Huynh (MD/PhD student, Paek Lab, University of Arizona)
“Role of FOXO transcription factor dynamics in determining cell fates”

Speaker 2: Megan McClean, PhD (Assistant Professor, University of Wisconsin)
“Single-cell measurement and control to unravel yeast gene expression heterogeneity”


August 19th:
Speaker 1: Christian Schröter, PhD (Research Group Leader, Max Planck Institute of Molecular Physiology)
“A new type of signaling dynamics downstream of FGF in embryonic stem cells”

Speaker 2: Allyson Sgro, PhD (Assistant Professor, Boston University)
“Connecting single-cell signaling dynamics to multicellular behaviors”


August 12th:
Speaker 1: Elizabeth Jose (Graduate Student, Paek lab, University of Arizona)
“Temporal coordination of Foxo, p53, and Nrf2 activation in response to oxidative stress”

Speaker 2: Gary Mo, PhD (Assistant Professor, University of Illinois at Chicago)
“Looking at Membrane Pore Signaling”


August 5th:
Speaker 1: Zhibo Zhang, PhD (Postdoc, Teruel Lab, Weil Cornell Medicine)
“The cell-intrinsic circadian clock gates fat cell differentiation commitment”

Speaker 2: Yaron Antebi, PhD (Principle Investigator, Weizmann Institute)
“The combinatorial logic of the BMP pathway”


July 29th:
Speaker 1: Claire Armstrong (Graduate student, Spencer Lab, University of Colorado)
“Replication-dependent histone biosynthesis is coupled to cell-cycle commitment”

Speaker 2: Qiong Yang, PhD (Assistant Professor, University of Michigan)
“Building a synthetic cell: Cell cycle robustness and hysteresis to cytoplasmic density variation”


July 22nd:
Speaker 1: Huy Vo, PhD (Postdoc, Munsky lab, Colorado State University)
Speaker 2: Michelle Mendoza, PhD (Assistant Professor, University of Utah)


July 15th:
Speaker 1: James Cornwell, PhD (Postdoc, Cappell lab, NCI)
Speaker 2: Songon “Song” An, PhD (Associate Professor, University of Maryland)


July 8th:
Speaker 1: Amy Peterson (Graduate Student, Regot lab, Johns Hopkins University)
Speaker 2: Gregor Neuert (Associate Professor, Vanderbilt University)


July 1st:
Abhineet Ram (Graduate student, Albeck Lab, UC Davis)
Silvia Santos, PhD (Group Leader, Crick Institute)
15:30GMT/ 11:30am EDT/ 8:30am PDT


June 24th: A double-dose of the Morrison (Rehm) lab!
Nadine Pollak, PhD (Scientific Staff, Morrison Lab, University of Stuttgart)
Markus Morrison (Rehm), PhD (Professor, University of Stuttgart)
15:30GMT/ 11:30am EDT/ 8:30am PDT


Join us June 17th for two new talks about signaling dynamics:
Maciej Dobrzynski, PhD (postdoc, Pertz lab, Universitat Bern)
Jeremie Roux, PhD (Associate Researcher, Universite Cote d’Azur)
15:30GMT/ 11:30am EDT/ 8:30am PDT


Our 2021 seminar series kicks off June 3! We will have two excellent keynote speakers followed by online social events to jumpstart this years InSiDE talks.
Come join us!

June 3: Keynote: Dr. Michiyuki Matsuda, Kyoto University
(*note special start time of 23:30 GMT/7:30pm EDT/4:30pm PDT)
Following the seminar, there will be an online social event on gather.town

June 10: Keynote: Dr. Galit Lahav, Harvard Medical School
(Seminar begins at 15:30 GMT/11:30am EDT/8:30am PDT)
Following the seminar, there will be an online poster session on gather.town at 16:30 GMT
Click Here to register to present a poster. Registration closes June 4.