Reflections on the National Science Foundation's Understanding the Rules of Life Program: Proceedings of a Workshop Series (2023)
Chapter: Appendix C: URoL-Funded Projects
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Appendix B: Biographical Sketches for Workshop Planning Committee and Participants
Appendix C
Suggested Citation:
"Appendix C: URoL-Funded Projects." National Academies of Sciences, Engineering, and Medicine. 2023. Reflections on the National Science Foundation's Understanding the Rules of Life Program: Proceedings of a Workshop Series. Washington, DC: The National Academies Press.
doi: 10.17226/27020.
Appendix C
URoL-Funded Projects
| Project Name | PI Name | Co-PI Name |
|---|---|---|
| URoL: Epigenetics 1: Control by noncoding RNA | Xiaojun Tian | |
| Collaborative Research: URoL: Epigenetics 2: Revealing how epigenetic inheritance governs the environmental challenge response with transformative 3D genomics and machine learning | Ayan Chakrabartim, R. Keith Slotkin | Malia Gehan, Ulugbek Kamilov, Tao Ju, Sona Pandey, Blake Meyers, Christopher Topp |
| URoL: Epigenetics 1: Characterization and dissection of DNA methylation and animal color changes in an African cichlid | Sebastian Alvarado | Wei Fang |
| Collaborative Research: URoL: Epigenetics 2: Phase separated genome compartments as drivers of epigenetic phenotypes | Geeta Narlikar, Stavros Lomvardas | Carolyn Larabell |
| Collaborative Research: URoL: Epigenetics 2: Predicting phenotypic and eco-evolutionary consequences of environmental-energetic-epigenetic linkages | Ross Cunning, Jose Eirin-Lopez, Holly Moeller, Hollie Putnam, Steven Roberts | Roger Nisbet |
| URoL: Epigenetics 2: Reverse engineering human epigenetic machinery in yeast | Jef Boeke | Matthew Maurano |
| URoL: Epigenetics 2: Robustness and adaptability of the dynamic epigenome: A multiscale approach | Kaushik Ragunathan | Ahmad Khalil, Ryan Bailey, Julie Biteen, Peter Freddolino |
| Collaborative Research: CYBORG cells: Modular integration of synthetic organelles into living cells | Mary Elting, Jane Maienschein, Fred Chang, Saad Bhamla | |
| Collaborative Research: Booting up a mirror cell | Neal Devaraj, Farren Isaacs | |
| Collaborative Research: Bottom-up construction of a synthetic neuron and programmable neuronal network | Allen Po-Chih Liu, Taekjip Ha, Moumita Das, Sindy KY Tang, Barbara Harthorn, Chongli Yuan | |
| Collaborative Research: ProteoCell: The fat-free cell | Cheryl Kerfeld, Giovanna Ghirlanda, Barbara Harthorn, Christine Keating, Millicent Sullivan, Vincent Noireaux | |
| Collaborative Research: Life with an RNA genome | Jef Boeke, Erika Szymanski, Kaihang Wang, Joel Bader | |
| Collaborative Research: URoL: Epigenetics 2: Bumble bee cold tolerance across elevations: From epigenotype to phenotype across space, time, and levels of biological organization | Michael Dillon, Jeffrey Lozier | Janna Fierst, James Strange, Franco Basile |
| URoL: Epigenetics 1: Influence of environmental change on the epigenome and phenotypic plasticity in purple sea urchins | Marie Strader | Katherine Buckley |
| Collaborative Research: URoL: Epigenetics 1: Novel epitransciptomics tools to understand and modulate interactions of modified RNAs with protein readers and erasers | Lydia Contreras, Phanourios Tamamis | |
| URoL: Epigenetics 2: Profiling and functional dissection of the epitranscriptome in archaeal extremophiles | Thomas Santangelo | Schraga Schwartz, Todd Lowe, Gregory Robb, Jordan Meier |
| URoL: Epigenetics 1: Genomic and epigenetic determinants of nuclear morphology and mechanics | Eric Richards | Jan Lammerding |
Suggested Citation:
"Appendix C: URoL-Funded Projects." National Academies of Sciences, Engineering, and Medicine. 2023. Reflections on the National Science Foundation's Understanding the Rules of Life Program: Proceedings of a Workshop Series. Washington, DC: The National Academies Press.
doi: 10.17226/27020.
| Project Name | PI Name | Co-PI Name |
|---|---|---|
| URoL: Epigenetics 2: Connecting cell fate and epigenome drift through physical models of chromatin structure and dynamics | Timothy Downing | Andrew Spakowitz, Alistair Boettiger, Elizabeth Read |
| URoL: Epigenetics 2: Learning the rules of dynamic epigenetic regulation | Georg Seelig | Jeffrey Nivala |
| Collaborative Research URoL: Epigenetics 2: Epigenetic pathways to regulate homeostatic resilience: Model-based discovery of rules across diverse mammals | Diane Genereux, Valery Forbes, Allyson Hindle, Elinor Karlsson | Bruce Birren |
| MTM 2: The rules of microbiota colonization of the mammalian gut | Georg Gerber | Harris Wang |
| URoL: MTM 1: Chemistry of cnidarian symbiosis: microbiomes role in association, morphogenesis, and protection | Sandra Loesgen | Mark Martindale, Virginia Weis |
| Collaborative Research: URoL: Epigenetics 2: Epigenetics in development and evolution of primate brains | William Hopkins, Soojin Yi, Chet Sherwood | |
| Collaborative Research: MTM 2: Searching for general rules governing microbiome dynamics using anaerobic digesters as model systems | Jizhong Zhou, Mathew Leibold, Qiang He, Alan Hastings | Daliang Ning |
| MTM 1: Experimental framework for marine fish microbiomes through synthetic communities and multi-omic approaches | Eric Allen | Pieter Dorrestein |
| MTM 2: Drivers of functional redundancy across microbiomes | Barbara Campbell | Vidya Suseela, Feng Luo, Anna Seekatz, Sharon Bewick |
| MTM 1: Network properties of fungal-bacterial interactions: Predictive modeling and functional analysis of the Hawaiian Drosophila gut microbiome | Joanne Yew | Laura Tipton |
| Collaborative Research: MTM 1: Microbial genomic, transcriptomic, and survival response to common built environment lighting | Jonathan Eisen, Kevin Van Den Wymelenberg | |
| MTM 2: Combining structural informatics and crosslinking mass spectrometry to predict the key protein-protein interactions shaping symbiotic microbial communities | Peter Freddolino | Vincent Young, Philip Andrews, Yang Zhang |
| URoL: MTM 2: Defining the ecological and genomic properties that underlie microbiome sensitivity and resilience | Rebecca Vega Thurber | Maude David, Ryan Mueller, Xiaoli Fern, Thomas Sharpton |
| MTM 1: The sandy beach microbiome: physical, chemical and biological controls on diversity and function | Alexandria Boehm | Christopher Francis |
| Emerging Frontiers: Collaborative Research: MTM 2: Marine invertebrate microbiome assembly, diversification, and coevolution | Kent Hatch, Purushotham Bangalore, Zachary Freedman, Robert Thacker | Richard Hardy |
| Collaborative Research: MTM 2: Microbially-mediated epigenetic modifications alter host phenotypes | Julie Hotopp, Irene Newton | Richard Hardy |
| Collaborative Research: MTM 2: Using successional dynamics, biogeography, and experimental communities to examine mechanisms of plant-microbiome functional interactions | Leonora Bittleston, Zachary Freedman, Erica Young, Benjamin Baiser | |
| Collaborative Research: MIM: Defining the rules governing microbiome interactions critical for providing key ecosystem functions using a model diazotroph community | Elizabeth Kujawinski, Eric Webb | Mak Saito, Cameron Thrash, Naomi Levine |
Suggested Citation:
"Appendix C: URoL-Funded Projects." National Academies of Sciences, Engineering, and Medicine. 2023. Reflections on the National Science Foundation's Understanding the Rules of Life Program: Proceedings of a Workshop Series. Washington, DC: The National Academies Press.
doi: 10.17226/27020.
| Project Name | PI Name | Co-PI Name |
|---|---|---|
| Collaborative Research: MIM: Gut-inhabiting fungi influence structure and function of herptile microbiomes through horizontal gene transfer and novel metabolic function | Joseph Spatafora, Jason Stajich, Donald Walker | Kerry McPhail |
| Collaborative Research: MIM: Learning how mucus shapes and maintains microbiomes | Sujit Datta, Katharina Ribbeck, Jessica Mark Welch | |
| Collaborative Research: MIM: The impact of the fungal microbiome in metal tolerance and soil biogeochemical transformations | Gregory Bonito, Jose Cerrato, Debora Rodrigues | Adam Brown |
| Collaborative Research: MIM: Using multilayer interaction networks to predict microbiome assembly and function | Elena Litchman, Mason Porter | Christopher Klausmeier, Shannon Manning |
| MIM: A thermodynamic theory of microbiome assembly, adaptation and evolution evaluated using modular microbial environments | Eoin Brodie | Jinyun Tang, Frances Hellman, Lydia Sohn, Adam Deutschbauer |
| MIM: Deciphering and optimizing cross-domain interactions to increase productivity in high pH-high alkalinity microalgae communities | Robin Gerlach | Huyen Bui, Ross Carlson, Matthew Fields |
| MIM: Discovering in reverse—using isotopic translation of omics to reveal ecological interactions in microbiomes. | Jane Marks | Bruce Hungate, Toby Hocking, James Caporaso, Mary Power |
| MIM: Elucidating the rules of cooperation and resiliency in microbial communities through stochastic graph grammars | Devaki Bhaya, Todd Treangen | Luay Nakhleh, Santiago Segarra |
| MIM: Machine learning, systems modeling, and experimental approaches to understand the universal rules of life of microbiota using marine time series data | Fengzhu Sun | Yan Liu, Emily Zakem, Jinchi Lv, Jed Fuhrman |
| MIM: Microbial division of labor in polysaccharidedegrading communities | Stephen Lindemann | |
| MIM: Systematic dissection of complex synthetic gut bacterial communities | Kerwyn Huang | |
| MIM: Using machine learning and a model watershed to understand how microbes govern food web architecture and efficiency | Anthony Amend | Nicole Hynson, Matthew Medeiros, Peter Sadowski |
| Emerging Frontiers: Synthetic cells that can learn without evolution | James Carothers | Emma Frow, Irene Chen, Pamela Peralta-Yahya, Matthew Lakin |
| URofL: EN: Does re-wilding lead to re-wiring of gene expression and species interaction networks? | Daniel Bolnick | Tina Eliassi-Rad, Samuel Scarpino, Miaoyan Wang |
| URoL: EN Converging on the rules of emergence for preventing land use-induced spillover | Raina Plowright | Elizabeth Shanahan, Andrew Hoegh, Agnieszka Rynda-Apple, Isabella Cattadori |
| URoL: EN Quantifying the phytochemical landscape through Indigenous Knowledge, interaction diversity, genomics, and network dynamics | Lora Robinson | Tod Swanson, Lee Dyer, Christopher Jeffrey, Deena Schmidt |
| URoL: EN: Learning the rules of neuronal learning | Pamela Abshire | Ricardo Araneda, Timothy Horiuchi |
| URoL: EN: Toward a unified theory of regulatory functions and networks across biological and social systems | Hyejin Youn | Chuqiao Yang, Geoffrey West, Sidney Redner, Christopher Kempes |
Suggested Citation:
"Appendix C: URoL-Funded Projects." National Academies of Sciences, Engineering, and Medicine. 2023. Reflections on the National Science Foundation's Understanding the Rules of Life Program: Proceedings of a Workshop Series. Washington, DC: The National Academies Press.
doi: 10.17226/27020.
Suggested Citation:
"Appendix C: URoL-Funded Projects." National Academies of Sciences, Engineering, and Medicine. 2023. Reflections on the National Science Foundation's Understanding the Rules of Life Program: Proceedings of a Workshop Series. Washington, DC: The National Academies Press.
doi: 10.17226/27020.
Suggested Citation:
"Appendix C: URoL-Funded Projects." National Academies of Sciences, Engineering, and Medicine. 2023. Reflections on the National Science Foundation's Understanding the Rules of Life Program: Proceedings of a Workshop Series. Washington, DC: The National Academies Press.
doi: 10.17226/27020.
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