CDC-Authored Genomics and Precision Health Publications Database
Last data update: Jan 27, 2025. (Total: 6504 publications)
Query Trace: Maccannell D[original query] |
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Genomic surveillance for SARS-CoV-2 variants: Circulation of Omicron XBB and JN.1 lineages - United States, May 2023-September 2024
Ma KC , Castro J , Lambrou AS , Rose EB , Cook PW , Batra D , Cubenas C , Hughes LJ , MacCannell DR , Mandal P , Mittal N , Sheth M , Smith C , Winn A , Hall AJ , Wentworth DE , Silk BJ , Thornburg NJ , Paden CR . MMWR Morb Mortal Wkly Rep 2024 73 (42) 938-945 ![]() |
Infectious disease surveillance needs for the United States: lessons from Covid-19
Lipsitch M , Bassett MT , Brownstein JS , Elliott P , Eyre D , Grabowski MK , Hay JA , Johansson MA , Kissler SM , Larremore DB , Layden JE , Lessler J , Lynfield R , MacCannell D , Madoff LC , Metcalf CJE , Meyers LA , Ofori SK , Quinn C , Bento AI , Reich NG , Riley S , Rosenfeld R , Samore MH , Sampath R , Slayton RB , Swerdlow DL , Truelove S , Varma JK , Grad YH . Front Public Health 2024 12 1408193 ![]() |
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training
Griffiths EJ , Mendes I , Maguire F , Guthrie JL , Wee BA , Schmedes S , Holt K , Yadav C , Cameron R , Barclay C , Dooley D , MacCannell D , Chindelevitch L , Karsch-Mizrachi I , Waheed Z , Katz L , Petit Iii R , Dave M , Oluniyi P , Nasar MI , Raphenya A , Hsiao WWL , Timme RE . Microb Genom 2024 10 (6) ![]() |
Bacterial strain typing.
MacCannell D . Clin Lab Med 2013 33 (3) 629-50 |
Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications
Timme RE , Karsch-Mizrachi I , Waheed Z , Arita M , MacCannell D , Maguire F , Petit Iii R , Page AJ , Mendes CI , Nasar MI , Oluniyi P , Tyler AD , Raphenya AR , Guthrie JL , Olawoye I , Rinck G , O'Cathail C , Lees J , Cochrane G , Cummins C , Brister JR , Klimke W , Feldgarden M , Griffiths E . Microb Genom 2023 9 (12) ![]() |
Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group
Baker KS , Jauneikaite E , Nunn JG , Midega JT , Atun R , Holt KE , Walia K , Howden BP , Tate H , Okeke IN , Carattoli A , Hsu LY , Hopkins KL , Muloi DM , Wheeler NE , Aanensen DM , Mason LCE , Rodgus J , Hendriksen RS , Essack SY , Egyir B , Halpin AL , MacCannell DR , Campos J , Srikantiah P , Feasey NA , Peacock SJ . Lancet Microbe 2023 4 (12) e1035-e1039 ![]() |
Early detection and surveillance of the SARS-CoV-2 variant BA.2.86 - Worldwide, July-October 2023
Lambrou AS , South E , Ballou ES , Paden CR , Fuller JA , Bart SM , Butryn DM , Novak RT , Browning SD , Kirby AE , Welsh RM , Cornforth DM , MacCannell DR , Friedman CR , Thornburg NJ , Hall AJ , Hughes LJ , Mahon BE , Daskalakis DC , Shah ND , Jackson BR , Kirking HL . MMWR Morb Mortal Wkly Rep 2023 72 (43) 1162-1167 ![]() |
Genomic surveillance for SARS-CoV-2 variants: Circulation of Omicron lineages - United States, January 2022-May 2023
Ma KC , Shirk P , Lambrou AS , Hassell N , Zheng XY , Payne AB , Ali AR , Batra D , Caravas J , Chau R , Cook PW , Howard D , Kovacs NA , Lacek KA , Lee JS , MacCannell DR , Malapati L , Mathew S , Mittal N , Nagilla RR , Parikh R , Paul P , Rambo-Martin BL , Shepard SS , Sheth M , Wentworth DE , Winn A , Hall AJ , Silk BJ , Thornburg N , Kondor R , Scobie HM , Paden CR . MMWR Morb Mortal Wkly Rep 2023 72 (24) 651-656 |
Cryptic transmission of SARS-CoV-2 in Washington State.
Bedford T , Greninger AL , Roychoudhury P , Starita LM , Famulare M , Huang ML , Nalla A , Pepper G , Reinhardt A , Xie H , Shrestha L , Nguyen TN , Adler A , Brandstetter E , Cho S , Giroux D , Han PD , Fay K , Frazar CD , Ilcisin M , Lacombe K , Lee J , Kiavand A , Richardson M , Sibley TR , Truong M , Wolf CR , Nickerson DA , Rieder MJ , Englund JA , Hadfield J , Hodcroft EB , Huddleston J , Moncla LH , Müller NF , Neher RA , Deng X , Gu W , Federman S , Chiu C , Duchin J , Gautom R , Melly G , Hiatt B , Dykema P , Lindquist S , Queen K , Tao Y , Uehara A , Tong S , MacCannell D , Armstrong GL , Baird GS , Chu HY , Shendure J , Jerome KR . medRxiv 2020 ![]() |
Spike Gene Target Amplification in a Diagnostic Assay as a Marker for Public Health Monitoring of Emerging SARS-CoV-2 Variants - United States, November 2021-January 2023.
Scobie HM , Ali AR , Shirk P , Smith ZR , Paul P , Paden CR , Hassell N , Zheng XY , Lambrou AS , Kondor R , MacCannell D , Thornburg NJ , Miller J , Wentworth D , Silk BJ . MMWR Morb Mortal Wkly Rep 2023 72 (5) 125-127 ![]() |
Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.
Karthikeyan S , Levy JI , De Hoff P , Humphrey G , Birmingham A , Jepsen K , Farmer S , Tubb HM , Valles T , Tribelhorn CE , Tsai R , Aigner S , Sathe S , Moshiri N , Henson B , Mark AM , Hakim A , Baer NA , Barber T , Belda-Ferre P , Chacón M , Cheung W , Cresini ES , Eisner ER , Lastrella AL , Lawrence ES , Marotz CA , Ngo TT , Ostrander T , Plascencia A , Salido RA , Seaver P , Smoot EW , McDonald D , Neuhard RM , Scioscia AL , Satterlund AM , Simmons EH , Abelman DB , Brenner D , Bruner JC , Buckley A , Ellison M , Gattas J , Gonias SL , Hale M , Hawkins F , Ikeda L , Jhaveri H , Johnson T , Kellen V , Kremer B , Matthews G , McLawhon RW , Ouillet P , Park D , Pradenas A , Reed S , Riggs L , Sanders A , Sollenberger B , Song A , White B , Winbush T , Aceves CM , Anderson C , Gangavarapu K , Hufbauer E , Kurzban E , Lee J , Matteson NL , Parker E , Perkins SA , Ramesh KS , Robles-Sikisaka R , Schwab MA , Spencer E , Wohl S , Nicholson L , McHardy IH , Dimmock DP , Hobbs CA , Bakhtar O , Harding A , Mendoza A , Bolze A , Becker D , Cirulli ET , Isaksson M , Schiabor Barrett KM , Washington NL , Malone JD , Schafer AM , Gurfield N , Stous S , Fielding-Miller R , Garfein RS , Gaines T , Anderson C , Martin NK , Schooley R , Austin B , MacCannell DR , Kingsmore SF , Lee W , Shah S , McDonald E , Yu AT , Zeller M , Fisch KM , Longhurst C , Maysent P , Pride D , Khosla PK , Laurent LC , Yeo GW , Andersen KG , Knight R . Nature 2022 609 (7925) 101-108 |
Early detection of SARS-CoV-2 variants using traveler-based genomic surveillance at four US airports, September 2021- January 2022.
Wegrzyn RD , Appiah GD , Morfino R , Milford SR , Walker AT , Ernst ET , Darrow WW , Li SL , Robison K , MacCannell D , Dai D , Girinathan BP , Hicks AL , Cosca B , Woronoff G , Plocik AM , Simen BB , Moriarty L , Guagliardo SAJ , Cetron MS , Friedman CR . Clin Infect Dis 2023 76 (3) e540-e543 ![]() |
Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants - United States, June 2021-January 2022.
Lambrou AS , Shirk P , Steele MK , Paul P , Paden CR , Cadwell B , Reese HE , Aoki Y , Hassell N , Caravas J , Kovacs NA , Gerhart JG , Ng HJ , Zheng XY , Beck A , Chau R , Cintron R , Cook PW , Gulvik CA , Howard D , Jang Y , Knipe K , Lacek KA , Moser KA , Paskey AC , Rambo-Martin BL , Nagilla RR , Rethchless AC , Schmerer MW , Seby S , Shephard SS , Stanton RA , Stark TJ , Uehara A , Unoarumhi Y , Bentz ML , Burhgin A , Burroughs M , Davis ML , Keller MW , Keong LM , Le SS , Lee JS , Madden Jr JC , Nobles S , Owouor DC , Padilla J , Sheth M , Wilson MM , Talarico S , Chen JC , Oberste MS , Batra D , McMullan LK , Halpin AL , Galloway SE , MacCannell DR , Kondor R , Barnes J , MacNeil A , Silk BJ , Dugan VG , Scobie HM , Wentworth DE . MMWR Morb Mortal Wkly Rep 2022 71 (6) 206-211 ![]() |
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Griffiths EJ , Timme RE , Mendes CI , Page AJ , Alikhan NF , Fornika D , Maguire F , Campos J , Park D , Olawoye IB , Oluniyi PE , Anderson D , Christoffels A , da Silva AG , Cameron R , Dooley D , Katz LS , Black A , Karsch-Mizrachi I , Barrett T , Johnston A , Connor TR , Nicholls SM , Witney AA , Tyson GH , Tausch SH , Raphenya AR , Alcock B , Aanensen DM , Hodcroft E , Hsiao WWL , Vasconcelos ATR , MacCannell DR . Gigascience 2022 11 ![]() |
SARS-CoV-2 Genomic Surveillance Reveals Little Spread From a Large University Campus to the Surrounding Community.
Valesano AL , Fitzsimmons WJ , Blair CN , Woods RJ , Gilbert J , Rudnik D , Mortenson L , Friedrich TC , O'Connor DH , MacCannell DR , Petrie JG , Martin ET , Lauring AS . Open Forum Infect Dis 2021 8 (11) ofab518 ![]() |
Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 in High-Density Settings, Minnesota, USA, March-June 2020.
Lehnertz NB , Wang X , Garfin J , Taylor J , Zipprich J , VonBank B , Martin K , Eikmeier D , Medus C , Wiedinmyer B , Bernu C , Plumb M , Pung K , Honein MA , Carter R , MacCannell D , Smith KE , Como-Sabetti K , Ehresmann K , Danila R , Lynfield R . Emerg Infect Dis 2021 27 (8) 2052-2063 ![]() |
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse.
Konings F , Perkins MD , Kuhn JH , Pallen MJ , Alm EJ , Archer BN , Barakat A , Bedford T , Bhiman JN , Caly L , Carter LL , Cullinane A , de Oliveira T , Druce J , El Masry I , Evans R , Gao GF , Gorbalenya AE , Hamblion E , Herring BL , Hodcroft E , Holmes EC , Kakkar M , Khare S , Koopmans MPG , Korber B , Leite J , MacCannell D , Marklewitz M , Maurer-Stroh S , Rico JAM , Munster VJ , Neher R , Munnink BO , Pavlin BI , Peiris M , Poon L , Pybus O , Rambaut A , Resende P , Subissi L , Thiel V , Tong S , van der Werf S , von Gottberg A , Ziebuhr J , Van Kerkhove MD . Nat Microbiol 2021 6 (7) 821-823 |
Introduction, Transmission Dynamics, and Fate of Early SARS-CoV-2 Lineages in Santa Clara County, California.
Villarino E , Deng X , Kemper CA , Jorden MA , Bonin B , Rudman SL , Han GS , Yu G , Wang C , Federman S , Bushnell B , Wadford DA , Lin W , Tao Y , Paden CR , Bhatnagar J , MacCannell T , Tong S , Batson J , Chiu CY . J Infect Dis 2021 224 (2) 207-217 ![]() |
Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States.
Alpert T , Brito AF , Lasek-Nesselquist E , Rothman J , Valesano AL , MacKay MJ , Petrone ME , Breban MI , Watkins AE , Vogels CBF , Kalinich CC , Dellicour S , Russell A , Kelly JP , Shudt M , Plitnick J , Schneider E , Fitzsimmons WJ , Khullar G , Metti J , Dudley JT , Nash M , Beaubier N , Wang J , Liu C , Hui P , Muyombwe A , Downing R , Razeq J , Bart SM , Grills A , Morrison SM , Murphy S , Neal C , Laszlo E , Rennert H , Cushing M , Westblade L , Velu P , Craney A , Cong L , Peaper DR , Landry ML , Cook PW , Fauver JR , Mason CE , Lauring AS , St George K , MacCannell DR , Grubaugh ND . Cell 2021 184 (10) 2595-2604 e13 |
Cryptic transmission of SARS-CoV-2 in Washington state.
Bedford T , Greninger AL , Roychoudhury P , Starita LM , Famulare M , Huang ML , Nalla A , Pepper G , Reinhardt A , Xie H , Shrestha L , Nguyen TN , Adler A , Brandstetter E , Cho S , Giroux D , Han PD , Fay K , Frazar CD , Ilcisin M , Lacombe K , Lee J , Kiavand A , Richardson M , Sibley TR , Truong M , Wolf CR , Nickerson DA , Rieder MJ , Englund JA , Hadfield J , Hodcroft EB , Huddleston J , Moncla LH , Müller NF , Neher RA , Deng X , Gu W , Federman S , Chiu C , Duchin JS , Gautom R , Melly G , Hiatt B , Dykema P , Lindquist S , Queen K , Tao Y , Uehara A , Tong S , MacCannell D , Armstrong GL , Baird GS , Chu HY , Shendure J , Jerome KR . Science 2020 370 (6516) 571-575 ![]() |
STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.
Bharucha T , Oeser C , Balloux F , Brown JR , Carbo EC , Charlett A , Chiu CY , Claas ECJ , de Goffau MC , de Vries JJC , Eloit M , Hopkins S , Huggett JF , MacCannell D , Morfopoulou S , Nath A , O'Sullivan DM , Reoma LB , Shaw LP , Sidorov I , Simner PJ , Van Tan L , Thomson EC , van Dorp L , Wilson MR , Breuer J , Field N . Lancet Infect Dis 2020 20 (10) e251-e260 ![]() |
Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
Deng X , Gu W , Federman S , du Plessis L , Pybus OG , Faria N , Wang C , Yu G , Bushnell B , Pan CY , Guevara H , Sotomayor-Gonzalez A , Zorn K , Gopez A , Servellita V , Hsu E , Miller S , Bedford T , Greninger AL , Roychoudhury P , Starita LM , Famulare M , Chu HY , Shendure J , Jerome KR , Anderson C , Gangavarapu K , Zeller M , Spencer E , Andersen KG , MacCannell D , Paden CR , Li Y , Zhang J , Tong S , Armstrong G , Morrow S , Willis M , Matyas BT , Mase S , Kasirye O , Park M , Masinde G , Chan C , Yu AT , Chai SJ , Villarino E , Bonin B , Wadford DA , Chiu CY . Science 2020 369 (6503) 582-587 |
Pathogen Genomics in Public Health.
Armstrong GL , MacCannell DR , Taylor J , Carleton HA , Neuhaus EB , Bradbury RS , Posey JE , Gwinn M . N Engl J Med 2019 381 (26) 2569-2580 ![]() ![]() |
Platforms and Analytical Tools Used in Nucleic Acid Sequence-Based Microbial Genotyping Procedures.
MacCannell D . Microbiol Spectr 2019 7 (1) ![]() |
Next-Generation Sequencing of Infectious Pathogens.
Gwinn M , MacCannell D , Armstrong GL . JAMA 2019 321 (9) 893-894 ![]() ![]() |
Evolution and Transmission of Carbapenem-Resistant Klebsiella pneumoniae Expressing the blaOXA-232 Gene During an Institutional Outbreak Associated With Endoscopic Retrograde Cholangiopancreatography.
Yang S , Hemarajata P , Hindler J , Li F , Adisetiyo H , Aldrovandi G , Sebra R , Kasarskis A , MacCannell D , Didelot X , Russell D , Rubin Z , Humphries R . Clin Infect Dis 2017 64 (7) 894-901 |
Integrating advanced molecular technologies into public health.
Gwinn M , MacCannell DR , Khabbaz RF . J Clin Microbiol 2016 55 (3) 703-714 ![]() |
Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic.
Bowers JR , Kitchel B , Driebe EM , MacCannell DR , Roe C , Lemmer D , de Man T , Rasheed JK , Engelthaler DM , Keim P , Limbago BM . PLoS One 2015 10 (7) e0133727 |
Good laboratory practice for clinical next-generation sequencing informatics pipelines.
Gargis AS , Kalman L , Bick DP , da Silva C , Dimmock DP , Funke BH , Gowrisankar S , Hegde MR , Kulkarni S , Mason CE , Nagarajan R , Voelkerding KV , Worthey EA , Aziz N , Barnes J , Bennett SF , Bisht H , Church DM , Dimitrova Z , Gargis SR , Hafez N , Hambuch T , Hyland FC , Luna RA , MacCannell D , Mann T , McCluskey MR , McDaniel TK , Ganova-Raeva LM , Rehm HL , Reid J , Campo DS , Resnick RB , Ridge PG , Salit ML , Skums P , Wong LJ , Zehnbauer BA , Zook JM , Lubin IM . Nat Biotechnol 2015 33 (7) 689-93 |
Canonical Single Nucleotide Polymorphisms (SNPs) for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC) O157:H7.
Griffing SM , MacCannell DR , Schmidtke AJ , Freeman MM , Hyytia-Trees E , Gerner-Smidt P , Ribot EM , Bono JL . PLoS One 2015 10 (7) e0131967 |
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