Professor research guide
Research using quantitative experiments, statistical mechanics, information theory, nonequilibrium physics, and large-scale biological measurements to discover predictive principles in gene regulation, biological fidelity, active matter, and viral ecology.
Independent educational guide. Not affiliated with or endorsed by the universities, professors or laboratories described here. This collection reflects the material currently mapped on Socratic Learn.
Research using quantitative experiments, statistical mechanics, information theory, nonequilibrium physics, and large-scale biological measurements to discover predictive principles in gene regulation, biological fidelity, active matter, and viral ecology.
6 lessons · ~29 minutes
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Research primer
6 lessons · ~29 minutes
Count, model, predict, measure, and revise: a video-first introduction to gene regulation, regulatory genomics, biological fidelity, active matter, and quantitative viral ecology.
Identify local energy consumption in active materials.
Connect copy number, binding energy, fold-change, and ligand-dependent allostery.
Explain why fidelity requires mechanism-specific coupling and evidence.
Estimate biological quantities with units and order-of-magnitude reasoning.
Distinguish a minimal model, a fitted parameter, and a prospective prediction.
Connect motor interactions to emergent microtubule dynamics and measurements.
Distinguish equilibrium discrimination from driven processes.
Apply measurement-to-model reasoning while preserving causal limits.
Interpret information footprints without claiming protein identification.
Interpret viral-genomics and phage-ecology observations within their dataset.
Explain sequence-to-expression reporter measurements.
Relate statistical weights to occupancy under stated assumptions.
2005
Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published thermodynamic-model framework; a model is scoped by its assumptions.
2011
Garcia HG, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published expression measurements test copy-number and binding-energy predictions for simple repression.
2014
Jones DL, Brewster RC, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published single-cell measurements test promoter-architecture models of variability.
2018
Razo-Mejia M, Barnes SL, Belliveau NM, Chure G, Einav T, Lewis M, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published induction measurements; ligand parameters fitted in one strain support predictions for others, not a wholly parameter-free fit.
2026
Yang Z, Rousseau RJ, Mahdavi SD, Garcia HG, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published circuit dynamics connect molecular regulation to dynamical models.
2018
Belliveau NM, Barnes SL, Ireland WT, Jones DL, Sweredoski MJ, Moradian A, Hess S, Kinney JB, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published Sort-Seq and protein-identification pipeline; measurements have distinct roles.
2020
Ireland WT, Beeler SM, Flores-Bautista E, McCarty NS, Röschinger T, Belliveau NM, Sweredoski MJ, Moradian A, Kinney JB, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published Reg-Seq sequence-to-expression measurements; footprints require additional protein-identification evidence.
2024
Pan RW, Röschinger T, Faizi K, Garcia HG, Phillips R
Why this matters: MODEL PREDICTION: published theory-of-the-experiment study using synthetic expression patterns, not new measured regulatory data.
2024
Mahdavi SD, Salmon GL, Daghlian P, Garcia HG, Phillips R
Why this matters: MODEL PREDICTION: published graph-theory analysis of driven promoter responses; does not demonstrate arbitrary measured gene regulation.
2023
Banks RA, Galstyan V, Lee HJ, Hirokawa S, Ierokomos A, Ross TD, Bryant Z, Thomson M, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published collaborative measurements connect motor speed and processivity to assembly structure.
2025
Hirokawa S, Lee HJ, Banks RA, Duarte AI, Najma B, Thomson M, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published photobleached tracking measurements distinguish rearrangement from overall motion.
2018
Mahmoudabadi G, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published comparative viral-genome analysis supports distributions, not universal host assignments.
2023
Tadmor AD, Mahmoudabadi G, Foley HB, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published observational phage-family tracking in metagenomes; site association does not prove causal ecology.
2024
Mahmoudabadi G, Homyk K, Catching AB, Mahmoudabadi A, Foley HB, Tadmor AD, Phillips R
Why this matters: PHILLIPS-LAB PRIMARY RESULT: published oral phage classifier in a particular dataset; not universal biometrics.
2026
Ravasio R, Husain K, Evans CG, Phillips R, Ribezzi-Crivellari M, Szostak JW, Murugan A
Why this matters: COLLABORATIVE PRIMARY RESULT: published Murugan-led models and selection simulations, with polymerase data consistent with the hypothesis; not universal proofreading.
2025
Yang F, Liu S, Lee HJ, Phillips R, Thomson M
Why this matters: COLLABORATIVE PRIMARY RESULT: published Thomson-led programmable flow control in active materials.
2025
Yang F, Liu S, Wang H, Lee HJ, Phillips R, Thomson M
Why this matters: COLLABORATIVE PRIMARY RESULT: published Thomson-led geometry-dependent merging of gaps and cracks, not topological defects.
2025
Röschinger T, Lee HJ, Pan RW, Solini G, Faizi K, Quan B, Chou T-F, Mani M, Quake S, Phillips R
Why this matters: CURRENT PREPRINT: expanded reporter measurements; assay scope and protein identification limit interpretation. Not peer reviewed on the source audit/current lab list.
2026
Gökmen DE, Pan RW, Röschinger T, Quake S, Garcia HG, Phillips R, Vitelli V
Why this matters: CURRENT PREPRINT: collaborative informational-blueprint models infer condition-dependent regulatory architectures; predictions require validation.
2026
Duarte AI, Salmon GL, Lee HJ, Najma B, Ashok M, Hirokawa S, Postma HWC, Banks RA, Thomson M, Phillips R
Why this matters: CURRENT PREPRINT: measured energetic gradients with a motor-energy hypothesis; not established consensus about every active system.