Repositories list

• GC_AMR_Lineages

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 20, 2025May 20, 2025

• mtrD-resistance

  Public
  Code to reproduce analyses in Ma and Mortimer et al., 2020 ("Efflux pump antibiotic binding site mutations are associated with azithromycin nonsusceptibility in clinical Neisseria gonorrhoeae isolates").

  Jupyter Notebook

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  MIT License

  •0•0•0•0•Updated Apr 23, 2025Apr 23, 2025

• mtrC-GWAS

  Public
  Code to reproduce analyses in Ma and Mortimer et al., 2020 ("Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae").

  Gnuplot

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  MIT License

  •1•4•0•0•Updated Apr 23, 2025Apr 23, 2025

• rplD-conditional-gwas

  Public
  Code to reproduce analyses in Ma et al., 2020 ("Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae").

  Gnuplot

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  MIT License

  •0•3•0•0•Updated Apr 23, 2025Apr 23, 2025

• ct-nowcasting-review

  Public
  HTML

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  Creative Commons Attribution 4.0 International

  •0•2•0•0•Updated Nov 5, 2024Nov 5, 2024

• doxy-PEP_surveillance

  Public
  Python

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  MIT License

  •1•1•0•0•Updated Aug 28, 2024Aug 28, 2024

• iceberg

  Public
  Python

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  MIT License

  •1•2•0•0•Updated Aug 28, 2024Aug 28, 2024

• detecting-sarscov2-variants

  Public
  Python

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  MIT License

  •1•2•0•0•Updated Jul 11, 2024Jul 11, 2024

• wastewater_equity

  Public
  Data and code for "Assessment of sewer connectivity in the United States and its implications for equity in wastewater-based epidemiology"

  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 18, 2024Apr 18, 2024

• use-resistance-seasonality

  Public
  Code to reproduce analyses in Sun et al., 2022 ("Analysis of multiple bacterial species and antibiotic classes reveals large variation in the association between seasonal antibiotic use and resistance").

  R

  •1•3•0•0•Updated Mar 5, 2024Mar 5, 2024

• StrepPharyngitis_Public

  Public
  PostScript

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  MIT License

  •0•0•0•0•Updated Feb 2, 2024Feb 2, 2024

• Abx-Geography

  Public
  R

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  MIT License

  •1•0•0•0•Updated Jan 3, 2024Jan 3, 2024

• lsarp_gwas

  Public
  Python

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  MIT License

  •2•1•1•0•Updated Oct 12, 2023Oct 12, 2023

• CovidTreatment

  Public
  R

  •0•0•0•0•Updated May 8, 2023May 8, 2023

• doxyPEP_genomics

  Public
  Data and code associated with "A genomic perspective on the near-term impact of doxycycline post-exposure prophylaxis on Neisseria gonorrhoeae antimicrobial resistance"

  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 27, 2023Apr 27, 2023

• SC2-kinetics-immune-history

  Public
  R

  •0•1•0•0•Updated Nov 23, 2022Nov 23, 2022

• PoolPower

  Public
  MIT License

  •0•0•0•0•Updated Nov 2, 2022Nov 2, 2022

• abx-race-2021

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Aug 19, 2022Aug 19, 2022

• covid19-newborn-seroprevalence

  Public
  Code to reproduce analyses in Ma et al. 2020 ("Trends in SARS-CoV-2 seroprevalence in Massachusetts estimated from newborn screening specimens").

  Jupyter Notebook

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  MIT License

  •0•0•0•0•Updated Mar 21, 2022Mar 21, 2022

• pcn_tet_susceptibility_gwas

  Public
  Data and code for "Genome wide association studies define minimal set of loci for prediction of penicillin and tetracycline susceptibility in Neisseria gonorrhoeae"

  R

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  MIT License

  •0•3•2•0•Updated Feb 7, 2022Feb 7, 2022

• CtTrajectories_Omicron

  Public
  R

  •0•6•0•0•Updated Jan 17, 2022Jan 17, 2022

• CtTrajectories_AllVariants

  Public
  R

  •0•6•0•0•Updated Oct 6, 2021Oct 6, 2021

• LifeExpectancy

  Public
  R

  •1•0•0•0•Updated Aug 2, 2021Aug 2, 2021

• CtTrajectories

  Public
  R

  •3•7•1•0•Updated Jun 17, 2021Jun 17, 2021

• PCN-GWAS

  Public
  Metadata associated with analyses in Jessica J. Zhang's thesis ("Defining the genetic basis of penicillin resistance in Neisseria gonorrhoeae through linear regression and genome-wide association studies")

  MIT License

  •0•0•0•0•Updated Mar 22, 2021Mar 22, 2021

• COVID_NYC

  Public
  R

  •0•0•0•0•Updated Jul 30, 2020Jul 30, 2020

• GC_NYC

  Public
  Scripts and data for Mortimer et al. 2020 "The distribution and spread of susceptible and resistant Neisseria gonorrhoeae across demographic groups in a major metropolitan center"

  R

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  MIT License

  •0•0•0•0•Updated Apr 29, 2020Apr 29, 2020

• geography

  Public
  Code to reproduce figures from geography ms.

  HTML

  •0•0•0•0•Updated Dec 2, 2019Dec 2, 2019

• bmj_trends

  Public
  SAS code used in Olesen et al. BMJ 2019

  SAS

  •0•2•0•0•Updated Jul 25, 2019Jul 25, 2019

• abx-race

  Public archive
  Code to reproduce results from ms.

  R

  •0•0•0•0•Updated Nov 20, 2018Nov 20, 2018