Public Health Modeling Publications

Featured Publications

Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Warren JL, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Venkataraman A, Lu-Culligan A, Klein J, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman OE, Wong P, Yang Y, Bermejo S, Odio CD, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND, Ko AI. Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2. New England Journal Of Medicine 2020, 383: 1283-1286. PMID: 32857487, PMCID: PMC7484747, DOI: 10.1056/nejmc2016359.
Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamicsPeccia J, Zulli A, Brackney DE, Grubaugh ND, Kaplan EH, Casanovas-Massana A, Ko AI, Malik AA, Wang D, Wang M, Warren JL, Weinberger DM, Arnold W, Omer SB. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nature Biotechnology 2020, 38: 1164-1167. PMID: 32948856, PMCID: PMC8325066, DOI: 10.1038/s41587-020-0684-z.
Assessment of SARS-CoV-2 Screening Strategies to Permit the Safe Reopening of College Campuses in the United StatesPaltiel AD, Zheng A, Walensky RP. Assessment of SARS-CoV-2 Screening Strategies to Permit the Safe Reopening of College Campuses in the United States. JAMA Network Open 2020, 3: e2016818. PMID: 32735339, PMCID: PMC7395236, DOI: 10.1001/jamanetworkopen.2020.16818.
Estimation of Excess Deaths Associated With the COVID-19 Pandemic in the United States, March to May 2020Weinberger DM, Chen J, Cohen T, Crawford FW, Mostashari F, Olson D, Pitzer VE, Reich NG, Russi M, Simonsen L, Watkins A, Viboud C. Estimation of Excess Deaths Associated With the COVID-19 Pandemic in the United States, March to May 2020. JAMA Internal Medicine 2020, 180: 1336-1344. PMID: 32609310, PMCID: PMC7330834, DOI: 10.1001/jamainternmed.2020.3391.
Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United StatesFauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J, Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott IM, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoudhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell 2020, 181: 990-996.e5. PMID: 32386545, PMCID: PMC7204677, DOI: 10.1016/j.cell.2020.04.021.
Association of Serotype with Risk of Death Due to Pneumococcal Pneumonia: A Meta-AnalysisWeinberger DM, Harboe ZB, Sanders EA, Ndiritu M, Klugman KP, Rückinger S, Dagan R, Adegbola R, Cutts F, Johnson HL, O'Brien KL, Scott JA, Lipsitch M. Association of Serotype with Risk of Death Due to Pneumococcal Pneumonia: A Meta-Analysis. Clinical Infectious Diseases 2010, 51: 692-699. PMID: 20715907, PMCID: PMC2927802, DOI: 10.1086/655828.

2023

Assessing the global risk of typhoid outbreaks caused by extensively drug resistant Salmonella TyphiWalker J, Chaguza C, Grubaugh N, Carey M, Baker S, Khan K, Bogoch I, Pitzer V. Assessing the global risk of typhoid outbreaks caused by extensively drug resistant Salmonella Typhi. Nature Communications 2023, 14: 6502. PMID: 37845201, PMCID: PMC10579367, DOI: 10.1038/s41467-023-42353-9.
Incorporating data from multiple endpoints in the analysis of clinical trials: example from RSV vaccines.Prunas O, Willemsen J, Bont L, Pitzer V, Warren J, Weinberger D. Incorporating data from multiple endpoints in the analysis of clinical trials: example from RSV vaccines. Epidemiology 2023 PMID: 37793120, DOI: 10.1097/ede.0000000000001680.
Floods and Diarrhea Risk in Young Children in Low- and Middle-Income CountriesWang P, Asare E, Pitzer V, Dubrow R, Chen K. Floods and Diarrhea Risk in Young Children in Low- and Middle-Income Countries. JAMA Pediatrics 2023, 177 PMID: 37782513, PMCID: PMC10546297, DOI: 10.1001/jamapediatrics.2023.3964.
Racial/ethnic disparities in PM2.5-attributable cardiovascular mortality burden in the United StatesMa Y, Zang E, Opara I, Lu Y, Krumholz H, Chen K. Racial/ethnic disparities in PM2.5-attributable cardiovascular mortality burden in the United States. Nature Human Behaviour 2023, 1-10. PMID: 37653149, DOI: 10.1038/s41562-023-01694-7.
The Impact of Rapid Drug Susceptibility Tests on Gonorrhea Burden and Lifespan of Antibiotic Treatments: A Modeling Study Among Men Who Have Sex With Men in the United States.Yaesoubi R, Xi Q, Hsu K, Gift T, St Cyr S, Rönn M, Salomon J, Grad Y. The Impact of Rapid Drug Susceptibility Tests on Gonorrhea Burden and Lifespan of Antibiotic Treatments: A Modeling Study Among Men Who Have Sex With Men in the United States. American Journal Of Epidemiology 2023 PMID: 37625444, DOI: 10.1093/aje/kwad175.
The blossoming of methods and software in computational biologyGabhann F, Pitzer V, Papin J. The blossoming of methods and software in computational biology. PLOS Computational Biology 2023, 19: e1011390. PMID: 37590323, PMCID: PMC10434930, DOI: 10.1371/journal.pcbi.1011390.
Year-round RSV Transmission in the Netherlands Following the COVID-19 Pandemic - A Prospective Nationwide Observational and Modeling Study.Löwensteyn Y, Zheng Z, Rave N, Bannier M, Billard M, Casalegno J, Pitzer V, Wildenbeest J, Weinberger D, Bont L, Vermaas-van Putten M, Smit-Kleinlugtenbeld E, Peetsold M, van der Kuip M, van Goudoever H, van Keulen B, Boot A, Kloos R, van Gool S, Snepvangers Y, Kuijpers A, Menelik N, de Crom S, Miedema C, ten Tusscher G, van Giessen J, de Moor R, Faber M, Breukels M, Jaddoe V, Duijts L, Lutterman C, Vink I, Tramper-Stranders G, Oudshoorn A, Ritman A, Dubbink-Verheij G, Bolt J, Cakir C, Rietveld E, Bekhof J, Rings E, de Swart J, Driessen G, Doedens R, Nijssen L, van Onzenoort-Bokken L, Meijneke R, van Scherpenzeel M, Faber T, de Groof F, Schouten S, van de Zande J, de Coul M, Henriet S, Stol K, van Rossem M, Jacobs M, van Houten M, Zuurbier R, Plötz F, de Vries A, van der Heide R, van Boekholt A, de Jong G, Rashid A, Roelofs M, Illy K, Reijmerink N, van Dorth S, Schipper S, Rosias P, Teirlinck A. Year-round RSV Transmission in the Netherlands Following the COVID-19 Pandemic - A Prospective Nationwide Observational and Modeling Study. The Journal Of Infectious Diseases 2023 PMID: 37477906, DOI: 10.1093/infdis/jiad282.
Worldwide Index of Serotype-Specific Pneumococcal Antibody Responses (WISSPAR): A curated database of clinical trial dataPerniciaro S, Cooper-Wooton D, Knoll M, Weinberger D. Worldwide Index of Serotype-Specific Pneumococcal Antibody Responses (WISSPAR): A curated database of clinical trial data. Gates Open Research 2023, 7: 109. DOI: 10.12688/gatesopenres.14768.1.
CT With CTA Versus MRI in Patients Presenting to the Emergency Department With Dizziness: Analysis Using Propensity Score Matching.Tu L, Navaratnam D, Melnick E, Melnick E, Forman H, Venkatesh A, Malhotra A, Yaesoubi R, Sureshanand S, Sheth K, Mahajan A. CT With CTA Versus MRI in Patients Presenting to the Emergency Department With Dizziness: Analysis Using Propensity Score Matching. American Journal Of Roentgenology 2023 PMID: 37404082, DOI: 10.2214/ajr.23.29617.
The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomicsWang Z, Kim W, Wang Y, Yakubovich E, Dong C, Trail F, Townsend J, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. Frontiers In Fungal Biology 2023, 4: 1214537. DOI: 10.3389/ffunb.2023.1214537.
Global, regional, and national estimates of tuberculosis incidence and case detection among incarcerated individuals from 2000 to 2019: a systematic analysisMartinez L, Warren J, Harries A, Croda J, Espinal M, Olarte R, Avedillo P, Lienhardt C, Bhatia V, Liu Q, Chakaya J, Denholm J, Lin Y, Kawatsu L, Zhu L, Horsburgh C, Cohen T, Andrews J. Global, regional, and national estimates of tuberculosis incidence and case detection among incarcerated individuals from 2000 to 2019: a systematic analysis. The Lancet Public Health 2023, 8: e511-e519. PMID: 37393090, PMCID: PMC10323309, DOI: 10.1016/s2468-2667(23)00097-x.
COVID-19 Related Immunisation Disruptions from 2020-2030: Projecting Health Impact and Mitigation Strategies for 14 Pathogens Across 112 Low- and Middle-Income CountriesHartner A, Li X, Echeverria-Londono S, Roth J, Abbas K, Auzenbergs M, de Villiers M, Ferrari M, Fraser K, Fu H, Hallett T, Hinsley W, Jit M, Prasinou A, Moore S, Nayagam S, Papadopoulos T, Perkins T, Portnoy A, Tran Q, Vynnycky E, Winter A, Burrows H, Chen C, Clapham H, Deshpande A, Hauryski S, Huber J, Jean K, Kim C, Kim J, Koh J, Lopman B, Pitzer V, Tam Y, Lambach P, Sim S, Woodruff K, Ferguson N, Trotter C, Gaythorpe K. COVID-19 Related Immunisation Disruptions from 2020-2030: Projecting Health Impact and Mitigation Strategies for 14 Pathogens Across 112 Low- and Middle-Income Countries. 2023 DOI: 10.2139/ssrn.4492698.
Assessment of Regional Nursing Home Preparedness for and Regulatory Responsiveness to Wildfire Risk in the Western USFesta N, Throgmorton K, Davis-Plourde K, Dosa D, Chen K, Zang E, Kelly J, Gill T. Assessment of Regional Nursing Home Preparedness for and Regulatory Responsiveness to Wildfire Risk in the Western US. JAMA Network Open 2023, 6: e2320207. PMID: 37358851, PMCID: PMC10293909, DOI: 10.1001/jamanetworkopen.2023.20207.
Population-Level Health Effects of Involuntary Displacement of People Experiencing Unsheltered Homelessness Who Inject Drugs in US CitiesBarocas J, Nall S, Axelrath S, Pladsen C, Boyer A, Kral A, Meehan A, Savinkina A, Peery D, Bien M, Agnew-Brune C, Goldshear J, Chiang J, Linas B, Gonsalves G, Bluthenthal R, Mosites E, Wortley P, Todd J, Melton D, Flynn C, German D, Klevens M, Doherty R, O'Cleirigh C, Jimenez A, Clyde T, Poe J, Vaaler M, Deng J, Al-Tayyib A, Shodell D, Higgins E, Griffin V, Sanger C, Khuwaja S, Lopez Z, Padgett P, Kwa Sey E, Ma Y, Santacruz H, Brantley M, Mathews C, Marr J, Spencer E, Nixon W, Forrest D, Anderson B, Tate A, Abrego M, Robinson W, Barak N, Beckford J, Braunstein S, Rivera A, Carrillo S, Ibrahim A, Wogayehu A, Moraga L, Brady K, Shinefeld J, Nnumolu C, Menza T, Orellana E, Bhattari A, Flynn A, Chambers O, Ramos M, McFarland W, Lin J, Miller D, Miranda De Leon S, Rolon-Colon Y, Martinez M, Jaenicke T, Glick S, Kienzle J, Smith B, Reid T, Opoku J, Kuo I, Adams M, Baugher A, Broz D, Burnett J, Chambers S, Chapin-Bardales J, Denning P, Finlayson T, Handanagic S, Hickey T, Kanny D, Lee K, Lewis R, Morris E, Olansky E, Robbins T, Sionean C, Smith A, Teplinskaya A, Trujillo K, Wejnert C, Whiteman A, Xia M. Population-Level Health Effects of Involuntary Displacement of People Experiencing Unsheltered Homelessness Who Inject Drugs in US Cities. JAMA 2023, 329: 1478-1486. PMID: 37036716, PMCID: PMC10087093, DOI: 10.1001/jama.2023.4800.
Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert OpinionsRich S, Richards V, Mavian C, Magalis B, Grubaugh N, Rasmussen S, Dellicour S, Vrancken B, Carrington C, Fisk-Hoffman R, Danso-Odei D, Chacreton D, Shapiro J, Seraphin M, Hepp C, Black A, Dennis A, Trovão N, Vandamme A, Rasmussen A, Lauzardo M, Dean N, Salemi M, Prosperi M. Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions. JMIR Formative Research 2023, 7: e39409. PMID: 36848460, PMCID: PMC10131930, DOI: 10.2196/39409.
Changes in Population Immunity Against Infection and Severe Disease From Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variants in the United States Between December 2021 and November 2022Klaassen F, Chitwood M, Cohen T, Pitzer V, Russi M, Swartwood N, Salomon J, Menzies N. Changes in Population Immunity Against Infection and Severe Disease From Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variants in the United States Between December 2021 and November 2022. Clinical Infectious Diseases 2023, 77: 355-361. PMID: 37074868, PMCID: PMC10425195, DOI: 10.1093/cid/ciad210.
High Levels of Detection of Nonpneumococcal Species of Streptococcus in Saliva from Adults in the United StatesHislop M, Allicock O, Thammavongsa D, Mbodj S, Nelson A, Shaw A, Weinberger D, Wyllie A. High Levels of Detection of Nonpneumococcal Species of Streptococcus in Saliva from Adults in the United States. Microbiology Spectrum 2023, 11: e05207-22. PMID: 37067447, PMCID: PMC10269540, DOI: 10.1128/spectrum.05207-22.
Social Vulnerability and Groundwater Vulnerability to Contamination From Unconventional Hydrocarbon Extraction in the Appalachian BasinSoriano M, Warren J, Clark C, Johnson N, Siegel H, Deziel N, Saiers J. Social Vulnerability and Groundwater Vulnerability to Contamination From Unconventional Hydrocarbon Extraction in the Appalachian Basin. GeoHealth 2023, 7: e2022gh000758. PMID: 37064218, PMCID: PMC10100439, DOI: 10.1029/2022gh000758.
Associations between short-term exposure to PM2.5, NO2 and O3 pollution and kidney-related conditions and the role of temperature-adjustment specification: A case-crossover study in New York stateChu L, Chen K, Di Q, Crowley S, Dubrow R. Associations between short-term exposure to PM2.5, NO2 and O3 pollution and kidney-related conditions and the role of temperature-adjustment specification: A case-crossover study in New York state. Environmental Pollution 2023, 328: 121629. PMID: 37054868, DOI: 10.1016/j.envpol.2023.121629.
Persistence of Pneumococcal Carriage among Older Adults in the Community despite COVID-19 Mitigation MeasuresWyllie A, Mbodj S, Thammavongsa D, Hislop M, Yolda-Carr D, Waghela P, Nakahata M, Stahlfeld A, Vega N, York A, Allicock O, Wilkins G, Ouyang A, Siqueiros L, Strong Y, Anastasio K, Alexander-Parrish R, Arguedas A, Gessner B, Weinberger D. Persistence of Pneumococcal Carriage among Older Adults in the Community despite COVID-19 Mitigation Measures. Microbiology Spectrum 2023, 11: e04879-22. PMID: 37036377, PMCID: PMC10269788, DOI: 10.1128/spectrum.04879-22.
Abstract 126: Extreme selection constrains ability of EGFR-driven lung adenocarcinoma to diversify in response to erlotinib therapyFisk J, Gaffney S, Politi K, Gettinger S, de Miguel F, Townsend J. Abstract 126: Extreme selection constrains ability of EGFR-driven lung adenocarcinoma to diversify in response to erlotinib therapy. Cancer Research 2023, 83: 126-126. DOI: 10.1158/1538-7445.am2023-126.
Assessment of vaccine herd protection in a cluster-randomised trial of Vi conjugate vaccine against typhoid fever: results of further analysisKhanam F, Kim D, Liu X, Voysey M, Pitzer V, Zaman K, Pollard A, Qadri F, Clemens J. Assessment of vaccine herd protection in a cluster-randomised trial of Vi conjugate vaccine against typhoid fever: results of further analysis. EClinicalMedicine 2023, 58: 101925. PMID: 37090439, PMCID: PMC10114505, DOI: 10.1016/j.eclinm.2023.101925.
Cost-Effectiveness and Long-Term Savings of the Bright Bodies Intervention for Childhood ObesityPryor S, Savoye M, Nowicka P, Price G, Sharifi M, Yaesoubi R. Cost-Effectiveness and Long-Term Savings of the Bright Bodies Intervention for Childhood Obesity. Value In Health 2023, 26: 1183-1191. PMID: 36967028, PMCID: PMC10518029, DOI: 10.1016/j.jval.2023.03.006.
Transmission modeling to infer tuberculosis incidence prevalence and mortality in settings with generalized HIV epidemicsDodd P, Shaweno D, Ku C, Glaziou P, Pretorius C, Hayes R, MacPherson P, Cohen T, Ayles H. Transmission modeling to infer tuberculosis incidence prevalence and mortality in settings with generalized HIV epidemics. Nature Communications 2023, 14: 1639. PMID: 36964130, PMCID: PMC10037365, DOI: 10.1038/s41467-023-37314-1.
Increased HIV transmissions with reduced insurance coverage for HIV pre-exposure prophylaxis: Potential consequences of Braidwood Management v. BecerraPaltiel A, Ahmed A, Jin E, McNamara M, Freedberg K, Neilan A, Gonsalves G. Increased HIV transmissions with reduced insurance coverage for HIV pre-exposure prophylaxis: Potential consequences of Braidwood Management v. Becerra. Open Forum Infectious Diseases 2023 DOI: 10.1093/ofid/ofad139.
Development of treatment-decision algorithms for children evaluated for pulmonary tuberculosis: an individual participant data meta-analysisGunasekera K, Marcy O, Muñoz J, Lopez-Varela E, Sekadde M, Franke M, Bonnet M, Ahmed S, Amanullah F, Anwar A, Augusto O, Aurilio R, Banu S, Batool I, Brands A, Cain K, Carratalá-Castro L, Caws M, Click E, Cranmer L, García-Basteiro A, Hesseling A, Huynh J, Kabir S, Lecca L, Mandalakas A, Mavhunga F, Myint A, Myo K, Nampijja D, Nicol M, Orikiriza P, Palmer M, Sant'Anna C, Siddiqui S, Smith J, Song R, Thuong Thuong N, Ung V, van der Zalm M, Verkuijl S, Viney K, Walters E, Warren J, Zar H, Marais B, Graham S, Debray T, Cohen T, Seddon J. Development of treatment-decision algorithms for children evaluated for pulmonary tuberculosis: an individual participant data meta-analysis. The Lancet Child & Adolescent Health 2023, 7: 336-346. PMID: 36924781, PMCID: PMC10127218, DOI: 10.1016/s2352-4642(23)00004-4.
Clinical criteria to exclude acute vascular pathology on CT angiogram in patients with dizzinessTu L, Malhotra A, Venkatesh A, Taylor R, Sheth K, Yaesoubi R, Forman H, Sureshanand S, Navaratnam D. Clinical criteria to exclude acute vascular pathology on CT angiogram in patients with dizziness. PLOS ONE 2023, 18: e0280752. PMID: 36893103, PMCID: PMC9997874, DOI: 10.1371/journal.pone.0280752.
Cost-effectiveness analysis of typhoid conjugate vaccines in an outbreak setting: a modeling studyPhillips M, Antillon M, Bilcke J, Bar-Zeev N, Limani F, Debellut F, Pecenka C, Neuzil K, Gordon M, Thindwa D, Paltiel A, Yaesoubi R, Pitzer V. Cost-effectiveness analysis of typhoid conjugate vaccines in an outbreak setting: a modeling study. BMC Infectious Diseases 2023, 23: 143. PMID: 36890448, PMCID: PMC9993384, DOI: 10.1186/s12879-023-08105-2.
Toward a global virus genomic surveillance networkHill V, Githinji G, Vogels C, Bento A, Chaguza C, Carrington C, Grubaugh N. Toward a global virus genomic surveillance network. Cell Host & Microbe 2023, 31: 861-873. PMID: 36921604, PMCID: PMC9986120, DOI: 10.1016/j.chom.2023.03.003.
Predicting indirect effects of rotavirus vaccination programs on rotavirus mortality among children in 112 countriesKraay A, Chaney D, Deshpande A, Pitzer V, Lopman B. Predicting indirect effects of rotavirus vaccination programs on rotavirus mortality among children in 112 countries. Npj Vaccines 2023, 8: 32. PMID: 36871093, PMCID: PMC9985632, DOI: 10.1038/s41541-023-00632-y.
Increased HIV Transmissions With Reduced Insurance Coverage for HIV Preexposure Prophylaxis: Potential Consequences of Braidwood Management v. BecerraPaltiel A, Ahmed A, Jin E, McNamara M, Freedberg K, Neilan A, Gonsalves G. Increased HIV Transmissions With Reduced Insurance Coverage for HIV Preexposure Prophylaxis: Potential Consequences of Braidwood Management v. Becerra. Open Forum Infectious Diseases 2023, 10: ofad139. PMID: 37008565, PMCID: PMC10061554, DOI: 10.1093/ofid/ofad139.
Associations between short-term temperature exposure and kidney-related conditions in New York State: The influence of temperature metrics across four dimensionsChu L, Chen K, Crowley S, Dubrow R. Associations between short-term temperature exposure and kidney-related conditions in New York State: The influence of temperature metrics across four dimensions. Environment International 2023, 173: 107783. DOI: 10.1016/j.envint.2023.107783.
Temperature variability and birthweight: epidemiological evidence from AfricaWang P, O'Donnell K, Warren J, Dubrow R, Chen K. Temperature variability and birthweight: epidemiological evidence from Africa. Environment International 2023, 173: 107792. DOI: 10.1016/j.envint.2023.107792.
Lifetime quality-adjusted life years lost due to genital herpes acquired in the United States in 2018: a mathematical modeling studyYou S, Yaesoubi R, Lee K, Li Y, Eppink S, Hsu K, Chesson H, Gift T, Berruti A, Salomon J, Rönn M. Lifetime quality-adjusted life years lost due to genital herpes acquired in the United States in 2018: a mathematical modeling study. The Lancet Regional Health - Americas 2023, 19: 100427. DOI: 10.1016/j.lana.2023.100427.
Assessing Principal Causal Effects Using Principal Score MethodsMattei A, Forastiere L, Mealli F. Assessing Principal Causal Effects Using Principal Score Methods. 2023, 313-348. DOI: 10.1201/9781003102670-17.
The COVID-19 pandemic as an opportunity for unravelling the causative association between respiratory viruses and pneumococcus-associated disease in young children: a prospective studyDagan R, van der Beek B, Ben-Shimol S, Greenberg D, Shemer-Avni Y, Weinberger D, Danino D. The COVID-19 pandemic as an opportunity for unravelling the causative association between respiratory viruses and pneumococcus-associated disease in young children: a prospective study. EBioMedicine 2023, 90: 104493. PMID: 36857965, PMCID: PMC9970381, DOI: 10.1016/j.ebiom.2023.104493.
Direct and indirect mortality impacts of the COVID-19 pandemic in the United States, March 1, 2020 to January 1, 2022Lee W, Park S, Weinberger D, Olson D, Simonsen L, Grenfell B, Viboud C. Direct and indirect mortality impacts of the COVID-19 pandemic in the United States, March 1, 2020 to January 1, 2022. ELife 2023, 12: e77562. PMID: 36811598, PMCID: PMC9946455, DOI: 10.7554/elife.77562.
Magnetic bead-based separation of pneumococcal serotypesYork A, Huynh E, Mbodj S, Yolda-Carr D, Hislop M, Echlin H, Rosch J, Weinberger D, Wyllie A. Magnetic bead-based separation of pneumococcal serotypes. Cell Reports Methods 2023, 3: 100410. PMID: 36936076, PMCID: PMC10014298, DOI: 10.1016/j.crmeth.2023.100410.
Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approachDu H, Dong E, Badr H, Petrone M, Grubaugh N, Gardner L. Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approach. EBioMedicine 2023, 89: 104482. PMID: 36821889, PMCID: PMC9943054, DOI: 10.1016/j.ebiom.2023.104482.
The Estimated Lifetime Quality-Adjusted Life-Years Lost Due to Chlamydia, Gonorrhea, and Trichomoniasis in the United States in 2018Li Y, You S, Lee K, Yaesoubi R, Hsu K, Gift T, Chesson H, Berruti A, Salomon J, Rönn M. The Estimated Lifetime Quality-Adjusted Life-Years Lost Due to Chlamydia, Gonorrhea, and Trichomoniasis in the United States in 2018. The Journal Of Infectious Diseases 2023, 227: 1007-1018. PMID: 36806950, PMCID: PMC10112678, DOI: 10.1093/infdis/jiad047.
Methods for Assessing Spillover in Network-Based Studies of HIV/AIDS Prevention among People Who Use DrugsBuchanan A, Katenka N, Lee Y, Wu J, Pantavou K, Friedman S, Halloran M, Marshall B, Forastiere L, Nikolopoulos G. Methods for Assessing Spillover in Network-Based Studies of HIV/AIDS Prevention among People Who Use Drugs. Pathogens 2023, 12: 326. PMID: 36839598, PMCID: PMC9967280, DOI: 10.3390/pathogens12020326.
Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster doseFilardi B, Monteiro V, Schwartzmann P, do Prado Martins V, Zucca L, Baiocchi G, Malik A, Silva J, Hahn A, Chen N, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca R, Della Rosa Mendez R, Silveira D, Pinto A, Croda J, Yildirim I, Omer S, Ko A, Vermund S, Grubaugh N, Iwasaki A, Lucas C, Initiative Y, Vogels C, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W. Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose. Science Translational Medicine 2023, 15: eade6023. PMID: 36791210, DOI: 10.1126/scitranslmed.ade6023.
Patterns of Infectious Disease Associated With Injection Drug Use in Massachusetts.Gonsalves G, Paltiel A, Thornhill T, DeMaria A, Cranston K, Klevens R, Warren J. Patterns of Infectious Disease Associated With Injection Drug Use in Massachusetts. Clinical Infectious Diseases 2023, 76: 2134-2139. PMID: 36757712, PMCID: PMC10273381, DOI: 10.1093/cid/ciad073.
Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineagesOliveira G, Vogels C, Zolfaghari A, Saraf S, Klitting R, Weger-Lucarelli J, P Leon K, Ontiveros C, Agarwal R, Tsetsarkin K, Harris E, Ebel G, Wohl S, Grubaugh N, Andersen K. Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages. PLOS Neglected Tropical Diseases 2023, 17: e0011055. PMID: 36753510, PMCID: PMC9907835, DOI: 10.1371/journal.pntd.0011055.
Lifetime quality-adjusted life years lost due to genital herpes acquired in the United States in 2018: a mathematical modeling studyYou S, Yaesoubi R, Lee K, Li Y, Eppink S, Hsu K, Chesson H, Gift T, Berruti A, Salomon J, Rönn M. Lifetime quality-adjusted life years lost due to genital herpes acquired in the United States in 2018: a mathematical modeling study. The Lancet Regional Health - Americas 2023, 19: 100427. PMID: 36950038, PMCID: PMC10025423, DOI: 10.1016/j.lana.2023.100427.
Spatial modeling of Mycobacterium tuberculosis transmission with dyadic genetic relatedness dataWarren J, Chitwood M, Sobkowiak B, Colijn C, Cohen T. Spatial modeling of Mycobacterium tuberculosis transmission with dyadic genetic relatedness data. Biometrics 2023 PMID: 36745619, PMCID: PMC10404301, DOI: 10.1111/biom.13836.
Routine saliva testing for SARS-CoV-2 in children: Methods for partnering with community childcare centersRayack E, Askari H, Zirinsky E, Lapidus S, Sheikha H, Peno C, Kazemi Y, Yolda-Carr D, Liu C, Grubaugh N, Ko A, Wyllie A, Spatz E, Oliveira C, Bei A. Routine saliva testing for SARS-CoV-2 in children: Methods for partnering with community childcare centers. Frontiers In Public Health 2023, 11: 1003158. PMID: 36817891, PMCID: PMC9936085, DOI: 10.3389/fpubh.2023.1003158.
Associations Between Long-Term Air Pollutant Exposure and 30-Day All-Cause Hospital Readmissions in US Patients With StrokeTran P, Warren J, Leifheit E, Goldstein L, Lichtman J. Associations Between Long-Term Air Pollutant Exposure and 30-Day All-Cause Hospital Readmissions in US Patients With Stroke. Stroke 2023, 54: e126-e129. PMID: 36729388, DOI: 10.1161/strokeaha.122.042265.
Temperature variability and birthweight: Epidemiological evidence from AfricaWang P, O'Donnell K, Warren J, Dubrow R, Chen K. Temperature variability and birthweight: Epidemiological evidence from Africa. Environment International 2023, 173: 107792. PMID: 36841185, DOI: 10.1016/j.envint.2023.107792.
Cost‐Effectiveness of Weight‐Loss Interventions Prior to Total Knee Replacement for Patients With Class III ObesityKostic AM, Leifer VP, Selzer F, Hunter DJ, Paltiel AD, Chen AF, Robinson MK, Neogi T, Collins JE, Messier SP, Edwards RR, Katz JN, Losina E. Cost‐Effectiveness of Weight‐Loss Interventions Prior to Total Knee Replacement for Patients With Class III Obesity. Arthritis Care & Research 2023, 75: 1752-1763. PMID: 36250415, PMCID: PMC10375659, DOI: 10.1002/acr.25044.
Magnetic bead-based separation of pneumococcal serotypesYork A, Huynh E, Mbodj S, Yolda-Carr D, Hislop M, Echlin H, Rosch J, Weinberger D, Wyllie A. Magnetic bead-based separation of pneumococcal serotypes. Cell Reports Methods 2023, 3: 100410. DOI: 10.1016/j.crmeth.2023.100410.
Abstract WMP98: Associations Between Long-term Co, No2, O3, Pm2.5, And So2Exposure And 30-day All-cause Hospital Readmission Among Stroke Patients In The Us: 2014-2015Tran P, Leifheit E, Warren J, Goldstein L, Lichtman J. Abstract WMP98: Associations Between Long-term Co, No2, O3, Pm2.5, And So2Exposure And 30-day All-cause Hospital Readmission Among Stroke Patients In The Us: 2014-2015. Stroke 2023, 54: awmp98-awmp98. DOI: 10.1161/str.54.suppl_1.wmp98.
Powassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA - Volume 29, Number 2—February 2023 - Emerging Infectious Diseases journal - CDCHart C, Hassett E, Vogels C, Shapley D, Grubaugh N, Thangamani S. Powassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA - Volume 29, Number 2—February 2023 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2023, 29: 415-417. PMID: 36692472, PMCID: PMC9881768, DOI: 10.3201/eid2902.220410.
Planning for Mpox on a College Campus: A Model-Based Decision-Support Tool.Savinkina A, Chitwood M, Kwon J, Pitzer V, Gonsalves G, Paltiel A. Planning for Mpox on a College Campus: A Model-Based Decision-Support Tool. Annals Of Internal Medicine 2023, 176: 340-347. PMID: 36716454, PMCID: PMC10338074, DOI: 10.7326/m22-2734.
Confounding by Conception Seasonality in Studies of Temperature and Preterm Birth: A Simulation StudyHuang M, Strickland M, Richards M, Warren J, Chang H, Darrow L. Confounding by Conception Seasonality in Studies of Temperature and Preterm Birth: A Simulation Study. Epidemiology 2023, 34: 439-449. PMID: 36719763, DOI: 10.1097/ede.0000000000001588.
Associations between short-term temperature exposure and kidney-related conditions in New York State: The influence of temperature metrics across four dimensionsChu L, Chen K, Crowley S, Dubrow R. Associations between short-term temperature exposure and kidney-related conditions in New York State: The influence of temperature metrics across four dimensions. Environment International 2023, 173: 107783. PMID: 36841184, DOI: 10.1016/j.envint.2023.107783.
Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infectionChaguza C, Hahn A, Petrone M, Zhou S, Ferguson D, Breban M, Pham K, Peña-Hernández M, Castaldi C, Hill V, Initiative Y, Billig K, Earnest R, Fauver J, Kalinch C, Kerantzas N, Koch T, De Kumar B, Landry M, Ott I, Peaper D, Tikhonova I, Vogels C, Schulz W, Swanstrom R, Roberts S, Grubaugh N. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Reports Medicine 2023, 4: 100943. PMID: 36791724, PMCID: PMC9906997, DOI: 10.1016/j.xcrm.2023.100943.
Generating simple classification rules to predict local surges in COVID-19 hospitalizationsYaesoubi R, You S, Xi Q, Menzies N, Tuite A, Grad Y, Salomon J. Generating simple classification rules to predict local surges in COVID-19 hospitalizations. Health Care Management Science 2023, 26: 301-312. PMID: 36692583, PMCID: PMC9872755, DOI: 10.1007/s10729-023-09629-4.
Geographic and temporal trends in fentanyl-detected deaths in Connecticut, 2009–2019Lu H, Crawford F, Gonsalves G, Grau L. Geographic and temporal trends in fentanyl-detected deaths in Connecticut, 2009–2019. Annals Of Epidemiology 2023, 79: 32-38. PMID: 36669599, PMCID: PMC10163838, DOI: 10.1016/j.annepidem.2023.01.009.
Infection by SARS‐CoV‐2 with alternate frequencies of mRNA vaccine boostingTownsend J, Hassler H, Dornburg A. Infection by SARS‐CoV‐2 with alternate frequencies of mRNA vaccine boosting. Journal Of Medical Virology 2023, 95: e28461. PMID: 36602045, DOI: 10.1002/jmv.28461.
Estimating Causal Effects of Multi-Valued Treatments Accounting for Network Interference: Immigration Policies and Crime RatesTortú C, Crimaldi I, Mealli F, Forastiere L. Estimating Causal Effects of Multi-Valued Treatments Accounting for Network Interference: Immigration Policies and Crime Rates. Sociological Methods & Research 2023, 004912412211475. DOI: 10.1177/00491241221147503.
Comparative Transcriptomics of Fusarium graminearum and Magnaporthe oryzae Spore Germination Leading up To InfectionMiguel-Rojas C, Cavinder B, Townsend J, Trail F. Comparative Transcriptomics of Fusarium graminearum and Magnaporthe oryzae Spore Germination Leading up To Infection. MBio 2023, 14: e02442-22. PMID: 36598191, PMCID: PMC9973345, DOI: 10.1128/mbio.02442-22.
Estimated Testing, Tracing, and Vaccination Targets for Containment of the US Mpox OutbreakChitwood M, Kwon J, Savinkina A, Walker J, Bilinski A, Gonsalves G. Estimated Testing, Tracing, and Vaccination Targets for Containment of the US Mpox Outbreak. JAMA Network Open 2023, 6: e2250984. PMID: 36637825, PMCID: PMC9857202, DOI: 10.1001/jamanetworkopen.2022.50984.
Chapter 5 Measurement and meaning in gene expression evolutionDiaz R, Wang Z, Townsend J. Chapter 5 Measurement and meaning in gene expression evolution. 2023, 111-129. DOI: 10.1016/b978-0-323-91810-7.00008-x.
Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection studyCheemarla N, Hanron A, Fauver J, Bishai J, Watkins T, Brito A, Zhao D, Alpert T, Vogels C, Ko A, Schulz W, Landry M, Grubaugh N, van Dijk D, Foxman E. Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study. The Lancet Microbe 2023, 4: e38-e46. PMID: 36586415, PMCID: PMC9835789, DOI: 10.1016/s2666-5247(22)00296-8.

2022

Comparison of model predictions of typhoid conjugate vaccine public health impact and cost-effectivenessBurrows H, Antillón M, Gauld J, Kim J, Mogasale V, Ryckman T, Andrews J, Lo N, Pitzer V. Comparison of model predictions of typhoid conjugate vaccine public health impact and cost-effectiveness. Vaccine 2022, 41: 965-975. PMID: 36586741, PMCID: PMC9880559, DOI: 10.1016/j.vaccine.2022.12.032.
Identification and characterization of novel lineage 1 Powassan virus strains in New York StateLange R, Dupuis A, Prusinski M, Maffei J, Koetzner C, Ngo K, Backenson B, Oliver J, Vogels C, Grubaugh N, Kramer L, Ciota A. Identification and characterization of novel lineage 1 Powassan virus strains in New York State. Emerging Microbes & Infections 2022, 12: 2155585. PMID: 36503411, PMCID: PMC9788702, DOI: 10.1080/22221751.2022.2155585.
High-resolution spatiotemporal modeling of daily near-surface air temperature in Germany over the period 2000–2020Nikolaou N, Dallavalle M, Stafoggia M, Bouwer L, Peters A, Chen K, Wolf K, Schneider A. High-resolution spatiotemporal modeling of daily near-surface air temperature in Germany over the period 2000–2020. Environmental Research 2022, 219: 115062. PMID: 36535393, DOI: 10.1016/j.envres.2022.115062.
Prioritization of carceral spending in U.S. cities: Development of the Carceral Resource Index (CRI) and the role of race and income inequalitySkaathun B, Maviglia F, Vo A, McBride A, Seymour S, Mendez S, Gonsalves G, Beletsky L. Prioritization of carceral spending in U.S. cities: Development of the Carceral Resource Index (CRI) and the role of race and income inequality. PLOS ONE 2022, 17: e0276818. PMID: 36520883, PMCID: PMC9754598, DOI: 10.1371/journal.pone.0276818.
2205. Potential Causative Association between Respiratory Viruses and Pneumococcus-Associated Disease in Young Children in Israel: Lessons from the COVID-19 PandemicDagan R, van der Beek B, Greenberg D, Avni Y, Ben-Shimol S, Weinberger D. 2205. Potential Causative Association between Respiratory Viruses and Pneumococcus-Associated Disease in Young Children in Israel: Lessons from the COVID-19 Pandemic. Open Forum Infectious Diseases 2022, 9: ofac492.1824. PMCID: PMC9752790, DOI: 10.1093/ofid/ofac492.1824.
Residential and Race/Ethnicity Disparities in Heat Vulnerability in the United StatesManware M, Dubrow R, Carrión D, Ma Y, Chen K. Residential and Race/Ethnicity Disparities in Heat Vulnerability in the United States. GeoHealth 2022, 6: e2022gh000695. PMID: 36518814, PMCID: PMC9744626, DOI: 10.1029/2022gh000695.
Waning Effectiveness of the BNT162b2 Vaccine Against Infection in Adolescents in Israel.Prunas O, Weinberger D, Pitzer V, Gazit S, Patalon T. Waning Effectiveness of the BNT162b2 Vaccine Against Infection in Adolescents in Israel. Clinical Infectious Diseases 2022, 76: 113-118. PMID: 36484301, PMCID: PMC10202431, DOI: 10.1093/cid/ciac315.
Estimation of neutral mutation rates and quantification of somatic variant selection using canceffectsizeRMandell J, Cannataro V, Townsend J. Estimation of neutral mutation rates and quantification of somatic variant selection using canceffectsizeR. Cancer Research 2022, 83: 500-505. PMID: 36469362, PMCID: PMC9929515, DOI: 10.1158/0008-5472.can-22-1508.
Daily Rapid Antigen Exit Testing to Tailor University COVID-19 Isolation Policy - Volume 28, Number 12—December 2022 - Emerging Infectious Diseases journal - CDCEarnest R, Chen C, Chaguza C, Hahn A, Grubaugh N, Wilson M, . Daily Rapid Antigen Exit Testing to Tailor University COVID-19 Isolation Policy - Volume 28, Number 12—December 2022 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2022, 28: 2455-2462. PMID: 36417936, PMCID: PMC9707582, DOI: 10.3201/eid2812.220969.
Cost‐effectiveness of hepatitis C virus test‐and‐treat and risk reduction strategies among men who have sex with men living with HIV in FranceCastry M, Cousien A, Champenois K, Supervie V, Velter A, Ghosn J, Yazdanpanah Y, Paltiel A, Deuffic‐Burban S. Cost‐effectiveness of hepatitis C virus test‐and‐treat and risk reduction strategies among men who have sex with men living with HIV in France. Journal Of The International AIDS Society 2022, 25: e26035. PMID: 36451286, PMCID: PMC9712801, DOI: 10.1002/jia2.26035.
Genome Sequence of a Recombinant SARS-CoV-2 Lineage XAM (BA.1.1/BA.2.9) Strain from a Clinical Sample in Santo Domingo, Dominican RepublicPaulino-Ramírez R, Pham K, Breban M, Peguero A, Jabier M, Sánchez N, Eustate I, Ruiz I, Grubaugh N, Hahn A. Genome Sequence of a Recombinant SARS-CoV-2 Lineage XAM (BA.1.1/BA.2.9) Strain from a Clinical Sample in Santo Domingo, Dominican Republic. Microbiology Resource Announcements 2022, 12: e01113-22. PMID: 36448812, PMCID: PMC9872639, DOI: 10.1128/mra.01113-22.
Identification of Human Monkeypox Virus Genome Deletions That Impact Diagnostic AssaysGarrigues J, Hemarajata P, Lucero B, Alarcón J, Ransohoff H, Marutani A, Kim M, Marlowe E, Realegeno S, Kagan R, Montero C, Chen N, Grubaugh N, Vogels C, Green N. Identification of Human Monkeypox Virus Genome Deletions That Impact Diagnostic Assays. Journal Of Clinical Microbiology 2022, 60: e01655-22. PMID: 36445125, PMCID: PMC9769645, DOI: 10.1128/jcm.01655-22.
Population-level strategies for nirmatrelvir/ritonavir prescribing - a cost-effectiveness analysisSavinkina A, Paltiel A, Ross J, Gonsalves G. Population-level strategies for nirmatrelvir/ritonavir prescribing - a cost-effectiveness analysis. Open Forum Infectious Diseases 2022 DOI: 10.1093/ofid/ofac637.
Population-Level Strategies for Nirmatrelvir/Ritonavir Prescribing—A Cost-effectiveness AnalysisSavinkina A, Paltiel A, Ross J, Gonsalves G. Population-Level Strategies for Nirmatrelvir/Ritonavir Prescribing—A Cost-effectiveness Analysis. Open Forum Infectious Diseases 2022, 9: ofac637. PMID: 36589482, PMCID: PMC9792084, DOI: 10.1093/ofid/ofac637.
Impact of Temporary Storage Conditions on the Viability of Streptococcus pneumoniae in SalivaAllicock O, York A, Waghela P, Yolda-Carr D, Weinberger D, Wyllie A. Impact of Temporary Storage Conditions on the Viability of Streptococcus pneumoniae in Saliva. MSphere 2022, 7: e00331-22. PMID: 36409104, PMCID: PMC9769876, DOI: 10.1128/msphere.00331-22.
Does gabapentin provide benefit for patients with knee OA? A benefit-harm and cost-effectiveness analysisBensen G, Rogers A, Leifer V, Edwards R, Neogi T, Kostic A, Paltiel A, Collins J, Hunter D, Katz J, Losina E. Does gabapentin provide benefit for patients with knee OA? A benefit-harm and cost-effectiveness analysis. Osteoarthritis And Cartilage 2022, 31: 279-290. PMID: 36414225, PMCID: PMC9892279, DOI: 10.1016/j.joca.2022.07.013.
Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort studyHay J, Kissler S, Fauver J, Mack C, Tai C, Samant R, Connolly S, Anderson D, Khullar G, MacKay M, Patel M, Kelly S, Manhertz A, Eiter I, Salgado D, Baker T, Howard B, Dudley J, Mason C, Nair M, Huang Y, DiFiori J, Ho D, Grubaugh N, Grad Y. Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study. ELife 2022, 11: e81849. PMID: 36383192, PMCID: PMC9711520, DOI: 10.7554/elife.81849.
Global disparities in SARS-CoV-2 genomic surveillanceBrito A, Semenova E, Dudas G, Hassler G, Kalinich C, Kraemer M, Ho J, Tegally H, Githinji G, Agoti C, Matkin L, Whittaker C, Howden B, Sintchenko V, Zuckerman N, Mor O, Blankenship H, de Oliveira T, Lin R, Siqueira M, Resende P, Vasconcelos A, Spilki F, Aguiar R, Alexiev I, Ivanov I, Philipova I, Carrington C, Sahadeo N, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije K, Perkins M, van Kerkhove M, Hill S, Sabino E, Pybus O, Dye C, Bhatt S, Flaxman S, Suchard M, Grubaugh N, Baele G, Faria N. Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications 2022, 13: 7003. PMID: 36385137, PMCID: PMC9667854, DOI: 10.1038/s41467-022-33713-y.
Not only mutations but also tumorigenesis can be substantially attributed to DNA damage from reactive oxygen species in RUNX1::RUNX1T1-fusion-positive acute myeloid leukemiaMandell J, Fisk J, Cyrenne E, Xu M, Cannataro V, Townsend J. Not only mutations but also tumorigenesis can be substantially attributed to DNA damage from reactive oxygen species in RUNX1::RUNX1T1-fusion-positive acute myeloid leukemia. Leukemia 2022, 36: 2931-2933. PMID: 36369483, PMCID: PMC9712081, DOI: 10.1038/s41375-022-01752-5.
Placing human gene families into their evolutionary contextDornburg A, Mallik R, Wang Z, Bernal M, Thompson B, Bruford E, Nebert D, Vasiliou V, Yohe L, Yoder J, Townsend J. Placing human gene families into their evolutionary context. Human Genomics 2022, 16: 56. PMID: 36369063, PMCID: PMC9652883, DOI: 10.1186/s40246-022-00429-5.
Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniquesBaaijens J, Zulli A, Ott I, Nika I, van der Lugt M, Petrone M, Alpert T, Fauver J, Kalinich C, Vogels C, Breban M, Duvallet C, McElroy K, Ghaeli N, Imakaev M, Mckenzie-Bennett M, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer M, Simen B, Hanage W, Grubaugh N, Peccia J, Baym M. Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques. Genome Biology 2022, 23: 236. PMID: 36348471, PMCID: PMC9643916, DOI: 10.1186/s13059-022-02805-9.
Predicting vaccine effectiveness against invasive pneumococcal disease in children using immunogenicity dataRyman J, Weaver J, Hu T, Weinberger D, Yee K, Sachs J. Predicting vaccine effectiveness against invasive pneumococcal disease in children using immunogenicity data. Npj Vaccines 2022, 7: 140. PMID: 36344529, PMCID: PMC9640717, DOI: 10.1038/s41541-022-00538-1.
Short-term exposure to air pollution and mental disorders: a case-crossover study in New York CityYoo E, Roberts J, Eum Y, Li X, Chu L, Wang P, Chen K. Short-term exposure to air pollution and mental disorders: a case-crossover study in New York City. Environmental Research Health 2022, 1: 015001. DOI: 10.1088/2752-5309/ac6439.
Predicted effectiveness of vaccines and extended half-life monoclonal antibodies against RSV hospitalizations in childrenZheng Z, Weinberger DM, Pitzer VE. Predicted effectiveness of vaccines and extended half-life monoclonal antibodies against RSV hospitalizations in children. Npj Vaccines 2022, 7: 127. PMID: 36302926, PMCID: PMC9612629, DOI: 10.1038/s41541-022-00550-5.
Estimated incidence of respiratory hospitalizations attributable to RSV infections across age and socioeconomic groupsZheng Z, Warren JL, Shapiro ED, Pitzer VE, Weinberger DM. Estimated incidence of respiratory hospitalizations attributable to RSV infections across age and socioeconomic groups. Pneumonia 2022, 14: 6. PMID: 36280891, PMCID: PMC9592130, DOI: 10.1186/s41479-022-00098-x.
Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidencePoterek ML, Vogels CBF, Grubaugh ND, Ebel GD, Perkins T, Cavany SM. Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence. Royal Society Open Science 2022, 9: 220829. PMID: 36277835, PMCID: PMC9579765, DOI: 10.1098/rsos.220829.
Detection of pneumococcus during hospitalization for SARS-CoV-2Stahlfeld A, Glick L, Ott I, Craft S, Yolda-Carr D, Harden C, Nakahata M, Farhadian S, Grant L, Alexander-Parrish R, Arguedas A, Gessner B, Weinberger D, Wyllie A. Detection of pneumococcus during hospitalization for SARS-CoV-2. FEMS Microbes 2022, 3 DOI: 10.1093/femsmc/xtac026.
Detection of pneumococcus during hospitalization for SARS-CoV-2Stahlfeld A, Glick L, Ott I, Craft S, Yolda-Carr D, Harden C, Nakahata M, Farhadian S, Grant L, Alexander-Parrish R, Arguedas A, Gessner B, Weinberger D, Wyllie A. Detection of pneumococcus during hospitalization for SARS-CoV-2. FEMS Microbes 2022, 3: xtac026. PMID: 37332510, PMCID: PMC10117745, DOI: 10.1093/femsmc/xtac026.
Quantifying Mycobacterium tuberculosis Transmission Dynamics Across Global Settings: A Systematic Analysis.Smith J, Cohen T, Dowdy D, Shrestha S, Gandhi NR, Hill AN. Quantifying Mycobacterium tuberculosis Transmission Dynamics Across Global Settings: A Systematic Analysis. American Journal Of Epidemiology 2022, 192: 133-145. PMID: 36227246, PMCID: PMC10144641, DOI: 10.1093/aje/kwac181.
Bivalent mRNA vaccine booster induces robust antibody immunity against Omicron lineages BA.2, BA.2.12.1, BA.2.75 and BA.5Fang Z, Monteiro VS, Hahn AM, Grubaugh ND, Lucas C, Chen S. Bivalent mRNA vaccine booster induces robust antibody immunity against Omicron lineages BA.2, BA.2.12.1, BA.2.75 and BA.5. Cell Discovery 2022, 8: 108. PMID: 36220819, PMCID: PMC9552143, DOI: 10.1038/s41421-022-00473-4.
Re-evaluating the health impact and cost-effectiveness of tuberculosis preventive treatment for modern HIV cohorts on antiretroviral therapy: a modelling analysis using data from TanzaniaZhu J, Lyatuu G, Sudfeld CR, Kiravu A, Sando D, Machumi L, Minde J, Chisonjela F, Cohen T, Menzies NA. Re-evaluating the health impact and cost-effectiveness of tuberculosis preventive treatment for modern HIV cohorts on antiretroviral therapy: a modelling analysis using data from Tanzania. The Lancet Global Health 2022, 10: e1646-e1654. PMID: 36240830, PMCID: PMC9553191, DOI: 10.1016/s2214-109x(22)00372-2.
Trends in non-COVID-19 hospitalizations prior to and during the COVID-19 pandemic period, United States, 2017–2021Cassell K, Zipfel CM, Bansal S, Weinberger DM. Trends in non-COVID-19 hospitalizations prior to and during the COVID-19 pandemic period, United States, 2017–2021. Nature Communications 2022, 13: 5930. PMID: 36209210, PMCID: PMC9546751, DOI: 10.1038/s41467-022-33686-y.
Predicting the long-term impact of rotavirus vaccination in 112 countries from 2006 to 2034: A transmission modeling analysisKraay A, Steele M, Baker J, Hall E, Deshpande A, Saidzosa B, Mukaratirwa A, Boula A, Mpabalwani E, Kiulia N, Tsolenyanu E, Enweronu-Laryea C, Abebe A, Beyene B, Tefera M, Willilo R, Batmunkh N, Pastore R, Mwenda J, Antoni S, Cohen A, Pitzer V, Lopman B. Predicting the long-term impact of rotavirus vaccination in 112 countries from 2006 to 2034: A transmission modeling analysis. Vaccine 2022, 40: 6631-6639. PMID: 36210251, PMCID: PMC10351612, DOI: 10.1016/j.vaccine.2022.09.072.
End-of-life care trajectories among older adults with lung cancerDavidoff AJ, Canavan ME, Prsic E, Saphire M, Wang SY, Presley CJ. End-of-life care trajectories among older adults with lung cancer. Journal Of Geriatric Oncology 2022, 14: 101381. PMID: 36202695, PMCID: PMC9974538, DOI: 10.1016/j.jgo.2022.09.010.
Bayesian Model Averaging to Account for Model Uncertainty in Estimates of a Vaccine’s EffectivenessOliveira CR, Shapiro ED, Weinberger DM. Bayesian Model Averaging to Account for Model Uncertainty in Estimates of a Vaccine’s Effectiveness. Clinical Epidemiology 2022, 14: 1167-1175. PMID: 36281232, PMCID: PMC9587703, DOI: 10.2147/clep.s378039.

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