Sergei Pond’s notebooks | Observable

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Sergei Pond’s notebooks | Observable

Sergei Pond

@spond

172

4

8

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National and International Dimensions of HIV-1 Sequence Clusters in a Northern California Clinical Cohort

May 19, 2019

3

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Molecular clock dating of reservoir strains

Nov 21, 2018

3

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Multiple group RELAX analysis

Mar 20, 2019

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Multiple group RELAX analysis

Mar 12, 2019

1

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SD-PIRC NGS quality control

Mar 26, 2019

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SD-PIRC sequence QA

Feb 7, 2019

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Usual vs unusual mutation analyses

May 20, 2024

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Dating OGV HIV strains

Nov 8, 2019

1

1

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Node-level Slatkin-Maddison Support

Mar 20, 2020

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Preliminary analysis of the CONDESA molecular transmission network

May 13, 2019

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Visualizing pairwise TN93 distances

Aug 20, 2019

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Preliminary analysis of the San Diego PIRC molecular transmission network

May 31, 2019

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Feb 8, 2023

1

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Two sample t-test

Jun 11, 2019

2

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K-means clustering algorithm

Nov 22, 2022

4

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PAML-style analyses summary

Jul 5, 2019

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HIV transmission network analysis

Jun 7, 2021

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Aug 29, 2019

2

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Figure 1 mtDNA paper

Oct 1, 2019

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Figure 1 mtDNA paper

Oct 3, 2019

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Clustering faculty applications

Nov 18, 2019

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Research and funding summary

Jul 3, 2024

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Multi-hit simulations

Jan 14, 2021

1

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Plotting MEME EBF on branches at individual sites

Mar 5, 2021

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Multi-hit simulations

Mar 8, 2020

1

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Example alignments for multihit paper

Feb 5, 2020

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Multihit paper empirical results for substitutions

Mar 9, 2020

1

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Multihit paper empirical results

Jan 12, 2021

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Genomic diversity and divergence of SARS-CoV-2/COVID-19

May 30, 2020

3

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Notice: this page has been deprecated in favor of a fully redesigned and updated version 2

Dec 22, 2020

11

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COVID table export

Mar 30, 2020

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Apr 7, 2020

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CpG deficiency in beta-coronaviruses

Apr 22, 2020

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SRRs with many mid-range variants (multiple infections)?

Sep 11, 2020

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Internal FEL on SARS-CoV-2 data

May 4, 2020

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Summary of SARS-CoV-2 genomic diversity

Sep 11, 2020

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Jul 31, 2020

1

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Testing recombination in the pandemic SARS-CoV-2 strains

Feb 9, 2021

2

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Genomic divergence of SARS-CoV-2 over time

Jun 29, 2020

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Mutation arrivals in SARS-CoV-2 genomes

Jun 18, 2020