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1

The effect of human mobility and control measures on the COVID-19 epidemic in China

Kraemer, Moritz U. G., Yang, Chia-Hung, Gutierrez, Bernardo, Wu, Chieh-Hsi, Klein, Brennan, Pigott, David M., du Plessis, Louis, Faria, Nuno R., Li, Ruoran, Hanage, William P., Brownstein, John S., La

Journal:

Year:

2020

Language:

english

File:

PDF, 3.11 MB

english, 2020

2

Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear

Grubaugh, Nathan D., Hanage, William P., Rasmussen, Angela L.

Journal:

Year:

2020

File:

PDF, 309 KB

2020

3

Serotype-specific problems associated with pneumococcal conjugate vaccination

Hanage, William P

Journal:

Future Microbiology

Year:

2008

Language:

english

File:

PDF, 284 KB

english, 2008

4

Weak Epistasis May Drive Adaptation in Recombining Bacteria

Arnold, Brian J., Gutmann, Michael U., Grad, Yonatan H., Sheppard, Samuel K., Corander, Jukka, Lipsitch, Marc, Hanage, William P.

Journal:

Year:

2018

Language:

english

File:

PDF, 7.18 MB

english, 2018

5

Historical Zoonoses and Other Changes in Host Tropism of Staphylococcus aureus, Identified by Phylogenetic Analysis of a Population Dataset

Shepheard, Marcus A., Fleming, Vicki M., Connor, Thomas R., Corander, Jukka, Feil, Edward J., Fraser, Christophe, Hanage, William P., Planet, Paul J.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.27 MB

english, 2013

6

Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics

Perron, Gabriel G., Whyte, Lyle, Turnbaugh, Peter J., Goordial, Jacqueline, Hanage, William P., Dantas, Gautam, Desai, Michael M., Brown, Sam Paul

Journal:

Year:

2015

Language:

english

File:

PDF, 1.94 MB

english, 2015

7

From bacterial genomics to clinical epidemiology: an interview with Bill Hanage

Hanage, William P.

Journal:

Year:

2018

Language:

english

File:

PDF, 496 KB

english, 2018

8

Leveraging Africa's preparedness towards the next phase of the COVID-19 pandemic

Senghore, Madikay, Savi, Merveille K, Gnangnon, BÃ©nÃ©dicte, Hanage, William P, Okeke, Iruka N

Journal:

The Lancet Global Health

Year:

2020

File:

PDF, 44 KB

2020

9

US racial and ethnic data for COVID-19 cases: still missing in action

Krieger, Nancy, Testa, Christian, Hanage, William P, Chen, Jarvis T

Journal:

Lancet (London, England)

Year:

2020

File:

PDF, 44 KB

2020

10

COVID-19: US federal accountability for entry, spread, and inequitiesâlessons for the future

Hanage, William P., Testa, Christian, Chen, Jarvis T., Davis, Letitia, Pechter, Elise, Seminario, Peg, Santillana, Mauricio, Krieger, Nancy

Journal:

European Journal of Epidemiology

Year:

2020

File:

PDF, 5.04 MB

2020

11

Epidemiology and risk factors forStaphylococcus aureuscolonization in children in the post-PCV7 era

Grace M Lee, Susan S Huang, Sheryl L Rifas-Shiman, Virginia L Hinrichsen, Stephen I Pelton, Ken Kleinman, William P Hanage, Marc Lipsitch, Alexander J McAdam, Jonathan A Finkelstein

Journal:

BMC Infectious Diseases

Year:

2009

Language:

english

File:

PDF, 547 KB

english, 2009

12

Fuzzy species among recombinogenic bacteria

William P Hanage, Christophe Fraser, Brian G Spratt

Journal:

Year:

2005

Language:

english

File:

PDF, 694 KB

english, 2005

13

Assigning strains to bacterial species via the internet

Cynthia J Bishop, David M Aanensen, Gregory E Jordan, Mogens Kilian, William P Hanage, Brian G Spratt

Journal:

Year:

2009

Language:

english

File:

PDF, 2.30 MB

english, 2009

14

Displaying the relatedness among isolates of bacterial species – the eBURST approach

Brian G. Spratt, William P. Hanage, Bao Li, David M. Aanensen, Edward J. Feil

Journal:

FEMS Microbiology Letters

Year:

2004

Language:

english

File:

PDF, 400 KB

english, 2004

15

The impact of homologous recombination on the generation of diversity in bacteria

William P. Hanage, Christophe Fraser, Brian G. Spratt

Journal:

Journal of Theoretical Biology

Year:

2006

Language:

english

File:

PDF, 566 KB

english, 2006

16

Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance

Rob J.L. Willems, William P. Hanage, Debra E. Bessen, Edward J. Feil

Journal:

FEMS Microbiology Reviews

Year:

2011

Language:

english

File:

PDF, 1.20 MB

english, 2011

17

Modelling infectious disease — time to think outside the box?

Wiles, Siouxsie, Hanage, William P., Frankel, Gad, Robertson, Brian

Journal:

Nature Reviews Microbiology

Year:

2006

Language:

english

File:

PDF, 335 KB

english, 2006

18

Bayesian modeling of recombination events in bacterial populations

Pekka Marttinen, Adam Baldwin, William P Hanage, Chris Dowson, Eshwar Mahenthiralingam, Jukka Corander

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.06 MB

english, 2008

19

Assessing the reliability of eBURST using simulated populations with known ancestry

Katherine ME Turner, William P Hanage, Christophe Fraser, Thomas R Connor, Brian G Spratt

Journal:

BMC Microbiology

Year:

2007

Language:

english

File:

PDF, 1.20 MB

english, 2007

20

Navigating the future of bacterial molecular epidemiology

Stephen Baker, William P Hanage, Kathryn E Holt

Journal:

Current Opinion in Microbiology

Year:

2010

Language:

english

File:

PDF, 535 KB

english, 2010

21

Re-emergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA

Gili Regev-Yochay, William P. Hanage, Krzysztof Trzcinski, Sheryl L. Rifas-Shiman, Grace Lee, Andrew Bessolo, Susan S. Huang, Stephen I. Pelton, Alexander J. McAdam, Jonathan A. Finkelstein, Marc Lips

Journal:

Year:

2010

Language:

english

File:

PDF, 415 KB

english, 2010

22

Serotype specific invasive capacity and persistent reduction in invasive pneumococcal disease

Inci Yildirim, William P. Hanage, Marc Lipsitch, Kimberly M. Shea, Abbie Stevenson, Jonathan Finkelstein, Susan S. Huang, Grace M. Lee, Ken Kleinman, S.I. Pelton

Journal:

Year:

2010

Language:

english

File:

PDF, 201 KB

english, 2010

23

Pneumococcal sequence type replacement among American Indian children: A comparison of pre- and routine-PCV7 eras

Jennifer R. Scott, William P. Hanage, Marc Lipsitch, Eugene V. Millar, Lawrence H. Moulton, Jason Hinds, Raymond Reid, Mathuram Santosham, Katherine L. O’Brien

Journal:

Year:

2012

Language:

english

File:

PDF, 392 KB

english, 2012

24

The relative contributions of recombination and point mutation to the diversification of bacterial clones

Brian G Spratt, William P Hanage, Edward J Feil

Journal:

Current Opinion in Microbiology

Year:

2001

Language:

english

File:

PDF, 60 KB

english, 2001

25

Streptococcus pneumoniae Contains 3 rlrA Pilus Variants That Are Clonally Related

Moschioni, Monica, Donati, Claudio, Muzzi, Alessandro, Masignani, Vega, Censini, Stefano, Hanage, William P., Bishop, Cynthia J., Reis, Joice Neves, Normark, Staffan, Henriques‐Normark, Birgitta, Cova

Journal:

The Journal of Infectious Diseases

Year:

2008

Language:

english

File:

PDF, 3.52 MB

english, 2008

26

No coexistence for free: Neutral null models for multistrain pathogens

Marc Lipsitch, Caroline Colijn, Ted Cohen, William P. Hanage, Christophe Fraser

Journal:

Year:

2009

Language:

english

File:

PDF, 663 KB

english, 2009

27

Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete

William P. Hanage, Jonathan A. Finkelstein, Susan S. Huang, Stephen I. Pelton, Abbie E. Stevenson, Ken Kleinman, Virginia L. Hinrichsen, Christophe Fraser

Journal:

Year:

2010

Language:

english

File:

PDF, 435 KB

english, 2010

28

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

Polz, Martin F., Alm, Eric J., Hanage, William P.

Journal:

Trends in Genetics

Year:

2013

Language:

english

File:

PDF, 440 KB

english, 2013

29

Population genomics of post-vaccine changes in pneumococcal epidemiology

Croucher, Nicholas J, Finkelstein, Jonathan A, Pelton, Stephen I, Mitchell, Patrick K, Lee, Grace M, Parkhill, Julian, Bentley, Stephen D, Hanage, William P, Lipsitch, Marc

Journal:

Nature Genetics

Year:

2013

Language:

english

File:

PDF, 1.81 MB

english, 2013

30

Fuzzy species revisited

William P Hanage

Journal:

Year:

2013

Language:

english

File:

PDF, 104 KB

english, 2013

31

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

Grad, Yonatan H, Kirkcaldy, Robert D, Trees, David, Dordel, Janina, Harris, Simon R, Goldstein, Edward, Weinstock, Hillard, Parkhill, Julian, Hanage, William P, Bentley, Stephen, Lipsitch, Marc

Journal:

The Lancet Infectious Diseases

Year:

2014

Language:

english

File:

PDF, 407 KB

english, 2014

32

The haunting reality of meningococcal meningitis

Hanage, William

Journal:

The Lancet Infectious Diseases

Year:

2013

Language:

english

File:

PDF, 308 KB

english, 2013

33

Mechanisms of genome evolution of Streptococcus

Andam, Cheryl P., Hanage, William P.

Journal:

Infection, Genetics and Evolution

Year:

2015

Language:

english

File:

PDF, 458 KB

english, 2015

34

Origin and Proliferation of Multiple-Drug Resistance in Bacterial Pathogens

Chang, Hsiao-Han, Cohen, Ted, Grad, Yonatan H., Hanage, William P., O'Brien, Thomas F., Lipsitch, Marc

Journal:

Microbiology and Molecular Biology Reviews

Year:

2015

Language:

english

File:

PDF, 901 KB

english, 2015

35

Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced

Chang, Qiuzhi, Stevenson, Abbie E, Croucher, Nicholas J, Lee, Grace M, Pelton, Stephen I, Lipsitch, Marc, Finkelstein, Jonathan A, Hanage, William P

Journal:

BMC Infectious Diseases

Year:

2015

Language:

english

File:

PDF, 822 KB

english, 2015

36

Diversity and Antibiotic Resistance among Nonvaccine Serotypes of Streptococcus pneumoniae Carriage Isolates in the Post–Heptavalent Conjugate Vaccine Era

Hanage, William P., Huang, Susan S., Lipsitch, Marc, Bishop, Cynthia J., Godoy, Daniel, Pelton, Stephen I., Goldstein, Richard, Huot, Heather, Finkelstein, Jonathan A.

Journal:

The Journal of Infectious Diseases

Year:

2007

Language:

english

File:

PDF, 607 KB

english, 2007

37

Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug-resistant pneumococcal clone

Croucher, Nicholas J, Hanage, William P, Harris, Simon R, McGee, Lesley, van der Linden, Mark, de Lencastre, Herminia, Sá-Leão, Raquel, Song, Jae-Hoon, Ko, Kwan, Beall, Bernard, Klugman, Keith P, Park

Journal:

Year:

2014

Language:

english

File:

PDF, 1.19 MB

english, 2014

38

The Important Role of Nontypable Streptococcus pneumoniae International Clones in Acute Conjunctivitis

Porat, Nurith, Greenberg, David, Givon‐Lavi, Noga, Shuval, Dror S., Trefler, Ronit, Segev, Orit, Hanage, William P., Dagan, Ron

Journal:

The Journal of Infectious Diseases

Year:

2006

Language:

english

File:

PDF, 2.26 MB

english, 2006

39

[IEEE 2014 IEEE International Conference on Big Data (Big Data) - Washington, DC, USA (2014.10.27-2014.10.30)] 2014 IEEE International Conference on Big Data (Big Data) - Random projection based clustering for population genomics

Tasoulis, Sotiris, Cheng, Lu, Valimaki, Niko, Croucher, Nicholas J., Harris, Simon R., Hanage, William P., Roos, Teemu, Corander, Jukka

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014

40

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data

Worby, Colin J., Lipsitch, Marc, Hanage, William P., Koelle, Katia

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 855 KB

english, 2014

41

Low Effective Dispersal of Asexual Genotypes in Heterogeneous Landscapes by the Endemic Pathogen Penicillium marneffei

Fisher, Matthew C., Hanage, William P., de Hoog, Sybren, Johnson, Elizabeth, Smith, Michael D., White, Nicholas J., Vanittanakom, Nongnuch

Journal:

Year:

2005

Language:

english

File:

PDF, 210 KB

english, 2005

42

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

Mostowy, Rafal, Croucher, Nicholas J., Hanage, William P., Harris, Simon R., Bentley, Stephen, Fraser, Christophe, Cooper, Vaughn S.

Journal:

Year:

2014

Language:

english

File:

PDF, 3.29 MB

english, 2014

43

Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach

Tang, Jing, Hanage, William P., Fraser, Christophe, Corander, Jukka, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 824 KB

english, 2009

44

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

Chewapreecha, Claire, Marttinen, Pekka, Croucher, Nicholas J., Salter, Susannah J., Harris, Simon R., Mather, Alison E., Hanage, William P., Goldblatt, David, Nosten, Francois H., Turner, Claudia, Tur

Journal:

Year:

2014

Language:

english

File:

PDF, 2.07 MB

english, 2014

45

Selective and Genetic Constraints on Pneumococcal Serotype Switching

Croucher, Nicholas J., Kagedan, Lisa, Thompson, Claudette M., Parkhill, Julian, Bentley, Stephen D., Finkelstein, Jonathan A., Lipsitch, Marc, Hanage, William P., Hughes, Diarmaid

Journal:

Year:

2015

Language:

english

File:

PDF, 1.78 MB

english, 2015

46

Antibiotics in agriculture and the risk to human health: how worried should we be?

Chang, Qiuzhi, Wang, Weike, Regev-Yochay, Gili, Lipsitch, Marc, Hanage, William P.

Journal:

Evolutionary Applications

Year:

2015

Language:

english

File:

PDF, 301 KB

english, 2015

47

Diversification of bacterial genome content through distinct mechanisms over different timescales

Croucher, Nicholas J., Coupland, Paul G., Stevenson, Abbie E., Callendrello, Alanna, Bentley, Stephen D., Hanage, William P.

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 5.39 MB

english, 2014

48

Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity

Li, Yuan, Croucher, Nicholas J, Thompson, Claudette M, Trzciński, Krzysztof, Hanage, William P, Lipsitch, Marc

Journal:

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

49

Interim results of an ecological experiment — Conjugate vaccination against the pneumococcus and serotype replacement

Hausdorff, William P, Hanage, William P

Journal:

Human Vaccines & Immunotherapeutics

Year:

2016

Language:

english

File:

PDF, 1.04 MB

english, 2016

50

Estimating the hospitalization burden associated with influenza and respiratory syncytial virus in New York City, 2003-2011

Goldstein, Edward, Greene, Sharon K., Olson, Donald R., Hanage, William P., Lipsitch, Marc

Journal:

Influenza and Other Respiratory Viruses

Year:

2015

Language:

english

File:

PDF, 124 KB

english, 2015