Rob Phillips Physical Biology Laboratory

2005

Transcriptional regulation by the numbers: models

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

Quantitative dissection of the simple repression input–output function

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

Promoter architecture dictates cell-to-cell variability in gene expression

Jones DL, Brewster RC, Phillips R

Why this matters: PHILLIPS-LAB PRIMARY RESULT: published single-cell measurements test promoter-architecture models of variability.

2018

Tuning transcriptional regulation through signaling: a predictive theory of allosteric induction

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

Dynamics of inducible genetic circuits

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

A systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

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

Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time

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

Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns

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

Flexibility and sensitivity in gene regulation out of equilibrium

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

Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies

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

Motor-driven microtubule diffusion in a photobleached dynamical coordinate system

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

A comprehensive and quantitative exploration of thousands of viral genomes

Mahmoudabadi G, Phillips R

Why this matters: PHILLIPS-LAB PRIMARY RESULT: published comparative viral-genome analysis supports distributions, not universal host assignments.

2023

Identification and spatio-temporal tracking of ubiquitous phage families in the human microbiome

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

Machine learning models can identify individuals based on a resident oral bacteriophage family

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

Evolution of error correction through a need for speed

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

Dynamic flow control through active matter programming language

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

Geometry-dependent defect merging induces bifurcated dynamics in active networks

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

Illuminating the uncharacterized regulatory genome of E. coli with massively parallel reporters

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

Informational blueprints reveal condition-dependent gene regulatory architectures

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

Energetic gradients emerge in developing motor-microtubule structures

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.

Intermediate

Test a minimal cell model

Computational simulation or public-data analysis

Compare a coarse-grained model with held-out synthetic observations.

Background

Relevant primer lessons, Basic Python and algebra

Data

{"Synthetic size, time, and copy-number measurements."}

Output

A unit-checked prediction plot and a separate report of fitted versus held-out error.

Independent learning idea, not offered or supervised by the lab. Use simulations or public non-identifying data only; no wet-lab work, microbial or phage culturing, genetic modification, clinical or forensic identification.

Intermediate

Explore simple repression

Computational simulation or public-data analysis

Vary copy number and binding energy in a stated equilibrium simulation.

Background

Relevant primer lessons, Basic Python and algebra

Data

{"Published model equations and synthetic inputs; no culturing."}

Output

Occupancy and fold-change plots plus assumptions and failure cases.

Independent learning idea, not offered or supervised by the lab. Use simulations or public non-identifying data only; no wet-lab work, microbial or phage culturing, genetic modification, clinical or forensic identification.

Intermediate

Interpret synthetic information footprints

Computational simulation or public-data analysis

Generate sequence-expression data with a known hidden regulatory region, then recover association.

Background

Relevant primer lessons, Basic Python and algebra

Data

{"Synthetic reporter sequence-expression tables following Pan et al."}

Output

A footprint with uncertainty and a statement that it does not independently identify a protein.

Independent learning idea, not offered or supervised by the lab. Use simulations or public non-identifying data only; no wet-lab work, microbial or phage culturing, genetic modification, clinical or forensic identification.

Intermediate

Simulate locally driven collective motion

Computational simulation or public-data analysis

Simulate interacting filaments with an explicit finite energy budget.

Background

Relevant primer lessons, Basic Python and algebra

Data

{"Toy motor–filament simulations and published open figures."}

Output

A motion plot comparing local interactions and energy removal; no perpetual-motion or central-control claim.

Independent learning idea, not offered or supervised by the lab. Use simulations or public non-identifying data only; no wet-lab work, microbial or phage culturing, genetic modification, clinical or forensic identification.

Intermediate

Compare public viral-genome distributions

Computational simulation or public-data analysis

Analyze public genome lengths or published aggregate phage-family distributions across sites.

Background

Relevant primer lessons, Basic Python and algebra

Data

{"Public non-identifying viral genome metadata and published aggregate tables."}

Output

A distribution plot with sampling, unknown-host, and association-versus-causation limits.

Independent learning idea, not offered or supervised by the lab. Use simulations or public non-identifying data only; no wet-lab work, microbial or phage culturing, genetic modification, clinical or forensic identification.