FINDING YOUR INNER MODELER                  
An NSF Workshop Year 6  
August 3-4, 2023
University of Alabama at Birmingham
Wednesday, August 2nd 6:00 – 8:00 PM
Meet and Greet Welcome Reception – The LAB Café at Hilton Hotel at UAB
808 20th St S, Birmingham, AL 35205
Thursday, August 3rd
Bevill Biomedical Research Building (BBRB) Room 170
845 19th St S Birmingham
8:15-9:00Registration
Assign people to mixed table groups with both data modelers and cell biologists
9:00-9:10Welcome and Meeting Overview: David Stone, UIC and Elizabeth Sztul, UAB
9:10-9:55Keynote Talk 1: Carlos Lopez, Altos Lab
Working Across Scales
9:55-10:25Project Presentation 1: Margarida Barroso, AMC and Xavier Intes, Rensselaer Polytechnic Inst.
Biology meets Engineering: Quantifying Drug-target Engagement in Vivo.
10:25-10:40Coffee Break
10:40-11:25Keynote Talk 2: Belinda Akpa, U of Tenn
Every Model has its Place: Combining Systems, Data-driven, and Generative Models for Therapeutic Design
11:25-12:10Project Presentation 2: David Stone, UIC and Andrew Mugler, U of Pittsburgh
Communicating Across Disciplines – How Yeast Cells Violate the Data Processing Inequality
12:10-1:10Catered Lunch
1:10-2:10Provocation: How to model across spatio-temporal scales
2:10-2:55Keynote Talk 3: Julien Berro, Yale
Measure. Model. Predict. Test. Repeat.
2:55-3:25Looking for a collaborator talks (2 talks, 15 minutes each)
Cecilia Alvarez, Universitat de Cordoba, Argentina;  Dynamics of Rab1b at the ER-Golgi Interface
Ashok Prasad, Colorado State; Morphological Modeling and Other Curiosities in Search of a Story
3:25-3:40Coffee Break
3:40-4:25Keynote talk 4: Eric Deeds, UCLA
A Lack of Distinct Cell Identities in Single-cell Data: Revisiting Waddington’s Landscape
4:25-6:30Poster Session and Happy Hour
Concurrent Session: Meet a Modeler consultation sessions: Eric Deeds, Elizabeth Read, Andrew Mugler, Belinda Akpa
Friday, August 4th
Bevill Biomedical Research Building (BBRB) Room 170
845 19th St S Birmingham
8:30-9:00Reconvene
9:00-9:05Briefing for the day: Reminder of the Vision
9:05-9:50Special presentation: Leonard Harris, University of Arkansas
Introduction to Computational Approaches and Tools for Cell Biologists
9:50-10:20Project Presentation 3: Elizabeth Read, UCI and Tim Downing, UCI
Bridging Modeling and Statistical Inference to Shed Light on Epigenetic Regulation and Cell Fate
10:20-10:35Coffee Break
10:35-11:20Keynote Talk 5:  Niall Mangan, Northwestern
Building Biological Models for Metabolic and Regulatory Networks: Traditional and Data-driven Approaches
11:20-11:50Project Presentation 4: Meghan Ferrall-Fairbanks, Camara Casson, Adriana Del Pino Herrera, University of Florida
Multi-disciplinary Training for Taking a Bite out of Cancer
11:50-12:50Catered Lunch
12:50-2:35Special Presentation: Graham Johnson, Allen Institute
Medical Illustration, Visual Analysis, and Modeling Driving Science and Intuition
2:20-2:50Looking for a collaborator talks (2 talks, 15 minutes each)
John Linehan, UNC; Model-based trajectory classification of anchored molecular motor-biopolymer interactions
Dipali Srivastava, North Carolina State University; Elucidating molecular mechanisms that control BRUTUS intracellular dynamics
3:05-3:20Coffee Break
3:20-4:00Town Hall Meeting
Closing Remarks: Elizabeth Sztul and David Stone  
4:00Depart for the airport or stay and enjoy a visit in Birmingham
Name University/Organization AffiliationGroup #Group “job”
Andrew Mugler University of Pittsburgh1Lead
Nial Mangan Northwestern 1
Cecilia Alvarez University of Cordoba, Argentina 1
Debangana Chakravorty UIC 1
Nolan English Oak Ridge National Lab1
Ghizelle Jane Abarro University of Tennessee Knoxville 1Scribe
Fatemeh Ghezelsofla Wright State University 1
Pitambar AcharyaWayne State University1
HaoSheng SunUAB1
Aaliya AhamedUAB1
Julien Berro Yale University2Lead
Ankur SaxenaUniversity of Illinois Chicago2Scribe
Elizabeth LeClairLurie Childrens’ Hospital2
Renee DaleDonald Danforth Plant Science Center2
Javid Azimi BoulaliBinghamton University2
Junhao GuUniversity of California, Irvine2
Alaaddin IbrahimyYale University2
Mehadi HasanUAB2
Sanaz HamiUAB2
Elizabeth Read UC Irvine3Lead
Dibyadeep DattaYale University3
Lynne NackeUIC3
Peter ChudinovUCSF3Scribe
Camara CassonUniversity of Florida3
Yacoub InnabiUniversity of California3
Ryan LeFebreUniversity of Pittsburgh3
Anil KadamUAB3
Eleanor CutcliffUAB3
Belinda AkpaOak Ridge National Laboratory & University of Tennessee4Lead
Tim DowningUC Irvine4
Margarida BarrosoAlbany Medical College4
Charles HodgensUniversity of Tennessee4Scribe
Shalmolee DasUIC4
John LinehanUniversity of North Carolina at Chapel Hill4
Ju-Won LeeUC Merced4
Shahid MukhtarUAB4
Dipak DulalUAB4
Eric DeedsUCLA5Lead
Ramin Goudarzi KarimStillman College5
Ashok PrasadColorado State University5Scribe
Dipali SrivastavaNorth Carolina State University5
Amin BoroomandUconn Health5
Kai HuUC Merced5
Tanya PelayoCalifornia State University5
Chenghui SongUAB5
Keren LiUAB5
Leonard HarrisUniversity of Arkansas6Lead
Christopher SolisUIC6Scribe
Yoshie HanzawaCalifornia State University Northridge6
Lingyun (Ivy) XiongUniversity of Southern California6
Amin BoroomandUniversity of California, Merced6
Adriana Del Pino HerreraUniversity of Florida6
Xinghang JiangUIC6
Amanda ClarkUAB6
Aqsa MajeedUAB6
Keshav SinghUniversity of Alabama at Birmingham7Lead
Xavier IntesRensselaer Polytechnic Institute7
Priyojit DasMassachusetts General Hospital – Harvard Medical School7Scribe
Mohammad NooranidoostFlorida State University7
Asees KaurUC Merced7
Melanie TuUCLA7
Deepak BastolaFlorida Atlantic University7
Carlos GallegosUAB7
Carmeliza NavascaUAB7
Jasim KhanUAB7
Carlos LopezLos Alamos Labs8Lead
Graham JohnsonAllen Institute for Cell Science8
Breanne SpartaUniversity of California Los Angeles8Scribe
Henry FreesSt. Louis University8
Alanda KellyUIC8
Gbocho TerasakiUC Merced8
Ariana YanceyUniversity of California, Santa Cruz8
Hassan QuamarulUAB8
Nicole RiddleUAB8
Nilesh KumarUAB8