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Appendix C: URoL-Funded Projects
Pages 78-80

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From page 78...
... 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 Ayan Chakrabartim, R Keith Slotkin Malia Gehan, Ulugbek how epigenetic inheritance governs the environmental Kamilov, Tao Ju, Sona challenge response with transformative 3D genomics and Pandey, Blake Meyers, machine learning Christopher Topp URoL: Epigenetics 1: Characterization and dissection of Sebastian Alvarado Wei Fang DNA methylation and animal color changes in an African cichlid Collaborative Research: URoL: Epigenetics 2: Phase Geeta Narlikar, Stavros Lomvardas Carolyn Larabell separated genome compartments as drivers of epigenetic phenotypes Collaborative Research: URoL: Epigenetics 2: Predicting Ross Cunning, Jose Eirin-Lopez, Holly Roger Nisbet phenotypic and eco-evolutionary consequences of Moeller, Hollie Putnam, Steven Roberts environmental-energetic-epigenetic linkages URoL: Epigenetics 2: Reverse engineering human Jef Boeke Matthew Maurano epigenetic machinery in yeast URoL: Epigenetics 2: Robustness and adaptability of the Kaushik Ragunathan Ahmad Khalil, Ryan dynamic epigenome: A multiscale approach Bailey, Julie Biteen, Peter Freddolino Collaborative Research: CYBORG cells: Modular Mary Elting, Jane Maienschein, Fred integration of synthetic organelles into living cells Chang, Saad Bhamla Collaborative Research: Booting up a mirror cell Neal Devaraj, Farren Isaacs Collaborative Research: Bottom-up construction of a Allen Po-Chih Liu, Taekjip Ha, Moumita synthetic neuron and programmable neuronal network 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 Michael Dillon, Jeffrey Lozier Janna Fierst, James cold tolerance across elevations: From epigenotype to Strange, Franco Basile phenotype across space, time, and levels of biological organization URoL: Epigenetics 1: Influence of environmental change Marie Strader Katherine Buckley on the epigenome and phenotypic plasticity in purple sea urchins Collaborative Research: URoL: Epigenetics 1: Novel Lydia Contreras, Phanourios Tamamis epitransciptomics tools to understand and modulate interactions of modified RNAs with protein readers and erasers URoL: Epigenetics 2: Profiling and functional dissection Thomas Santangelo Schraga Schwartz, Todd of the epitranscriptome in archaeal extremophiles Lowe, Gregory Robb, Jordan Meier URoL: Epigenetics 1: Genomic and epigenetic Eric Richards Jan Lammerding determinants of nuclear morphology and mechanics 78
From page 79...
... Appendix C 79 Project Name PI Name Co-PI Name URoL: Epigenetics 2: Connecting cell fate and epigenome Timothy Downing Andrew Spakowitz, drift through physical models of chromatin structure and Alistair Boettiger, dynamics Elizabeth Read URoL: Epigenetics 2: Learning the rules of dynamic Georg Seelig Jeffrey Nivala epigenetic regulation Collaborative Research URoL: Epigenetics 2: Epigenetic Diane Genereux, Valery Forbes, Allyson Bruce Birren pathways to regulate homeostatic resilience: Model-based Hindle, Elinor Karlsson discovery of rules across diverse mammals MTM 2: The rules of microbiota colonization of the Georg Gerber Harris Wang mammalian gut URoL: MTM 1: Chemistry of cnidarian symbiosis: Sandra Loesgen Mark Martindale, microbiomes role in association, morphogenesis, and Virginia Weis protection Collaborative Research: URoL: Epigenetics 2: Epigenetics William Hopkins, Soojin Yi, Chet in development and evolution of primate brains Sherwood Collaborative Research: MTM 2: Searching for general Jizhong Zhou, Mathew Leibold, Qiang Daliang Ning rules governing microbiome dynamics using anaerobic He, Alan Hastings digesters as model systems MTM 1: Experimental framework for marine fish Eric Allen Pieter Dorrestein microbiomes through synthetic communities and multiomic approaches MTM 2: Drivers of functional redundancy across Barbara Campbell Vidya Suseela, Feng microbiomes Luo, Anna Seekatz, Sharon Bewick MTM 1: Network properties of fungal-bacterial Joanne Yew Laura Tipton interactions: Predictive modeling and functional analysis of the Hawaiian Drosophila gut microbiome Collaborative Research: MTM 1: Microbial genomic, Jonathan Eisen, Kevin Van Den transcriptomic, and survival response to common built Wymelenberg environment lighting MTM 2: Combining structural informatics and Peter Freddolino Vincent Young, Philip crosslinking mass spectrometry to predict the key protein- Andrews, Yang Zhang protein interactions shaping symbiotic microbial communities URoL: MTM 2: Defining the ecological and genomic Rebecca Vega Thurber Maude David, Ryan properties that underlie microbiome sensitivity and Mueller, Xiaoli Fern, resilience Thomas Sharpton MTM 1: The sandy beach microbiome: physical, chemical Alexandria Boehm Christopher Francis and biological controls on diversity and function Emerging Frontiers: Collaborative Research: MTM 2: Kent Hatch, Purushotham Bangalore, Richard Hardy Marine invertebrate microbiome assembly, diversification, Zachary Freedman, Robert Thacker and coevolution Collaborative Research: MTM 2: Microbially-mediated Julie Hotopp, Irene Newton Richard Hardy epigenetic modifications alter host phenotypes Collaborative Research: MTM 2: Using successional Leonora Bittleston, Zachary Freedman, dynamics, biogeography, and experimental communities to Erica Young, Benjamin Baiser examine mechanisms of plant-microbiome functional interactions Collaborative Research: MIM: Defining the rules Elizabeth Kujawinski, Eric Webb Mak Saito, Cameron governing microbiome interactions critical for providing Thrash, Naomi Levine key ecosystem functions using a model diazotroph community continued
From page 80...
... Scarpino, Miaoyan Wang URoL: EN Converging on the rules of emergence for Raina Plowright Elizabeth Shanahan, preventing land use-induced spillover Andrew Hoegh, Agnieszka Rynda-Apple, Isabella Cattadori URoL: EN Quantifying the phytochemical landscape Lora Robinson Tod Swanson, Lee Dyer, through Indigenous Knowledge, interaction diversity, Christopher Jeffrey, genomics, and network dynamics Deena Schmidt URoL: EN: Learning the rules of neuronal learning Pamela Abshire Ricardo Araneda, Timothy Horiuchi URoL: EN: Toward a unified theory of regulatory Hyejin Youn Chuqiao Yang, Geoffrey functions and networks across biological and social West, Sidney Redner, systems Christopher Kempes


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