dissertation

Viral phylodynamics of

Sidney Bell

Bedford Lab

Molecular & Cellular Biology

Neher et al, PNAS 2016

\approx \sum{d_b}

\approx \sum{d_b}

Titer

between

+ avidity + potency

d_b

d_b

d_{1}

d_{1}

d_{2}

d_{2}

d_{3}

d_{3}

d_{4}

d_{4}

1.0

0.5

\hat{T_{ij}} = \sum{d_b} + v_i + s_j

\hat{T_{ij}} = \sum{d_b} + v_i + s_j

\sum_{i,j}(\hat{T_{ij}} - T{ij})^2 + \lambda \sum_{b}d_b + \gamma \sum_{i} v_i^2 + \delta \sum_{j} s_j^2

\sum_{i,j}(\hat{T_{ij}} - T{ij})^2 + \lambda \sum_{b}d_b + \gamma \sum_{i} v_i^2 + \delta \sum_{j} s_j^2

Learn these

Minimize

this

Predict titers

\hat{T_{ij}} = \sum{d_b} + v_i + s_j

\hat{T_{ij}} = \sum{d_b} + v_i + s_j

\sum_{i,j}(\hat{T_{ij}} - T{ij})^2 + \lambda \sum_{b}d_b + \gamma \sum_{i} v_i^2 + \delta \sum_{j} s_j^2

\sum_{i,j}(\hat{T_{ij}} - T{ij})^2 + \lambda \sum_{b}d_b + \gamma \sum_{i} v_i^2 + \delta \sum_{j} s_j^2

dTiter on each branch

avidity

potency

Predict titers

\hat{T_{ij}} = \sum{d_b} + v_i + s_j

\hat{T_{ij}} = \sum{d_b} + v_i + s_j

\sum_{i,j}(\hat{T_{ij}} - T{ij})^2 + \lambda \sum_{b}d_b + \gamma \sum_{i} v_i^2 + \delta \sum_{j} s_j^2

\sum_{i,j}(\hat{T_{ij}} - T{ij})^2 + \lambda \sum_{b}d_b + \gamma \sum_{i} v_i^2 + \delta \sum_{j} s_j^2

Squared Error

Minimize

this

L1 norm on branch effects

L2 norm on virus avidity & serum potency

dTiter on each branch

avidity

potency

Predict titers

Viral phylodynamics of host adaptation & antigenic evolution Sidney Bell Bedford Lab Molecular & Cellular Biology

Pearson R	0.79
Abs. Error	1.02