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1.

The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid-Type I IFN Signaling Axis.

Winkler, Emma S; Shrihari, Swathi; Hykes, Barry L; Handley, Scott A; Andhey, Prabhakar S; Huang, Yan-Jang S; Swain, Amanda; Droit, Lindsay; Chebrolu, Kranthi K; Mack, Matthias; Vanlandingham, Dana L; Thackray, Larissa B; Cella, Marina; Colonna, Marco; Artyomov, Maxim N; Stappenbeck, Thaddeus S; Diamond, Michael S.

Cell ; 182(4): 901-918.e18, 2020 08 20.

Artículo en Inglés | MEDLINE | ID: mdl-32668198

2.

Drowning in Viruses.

Handley, Scott A; Virgin, Herbert W.

Cell ; 177(5): 1084-1085, 2019 05 16.

Artículo en Inglés | MEDLINE | ID: mdl-31100262

3.

A potently neutralizing SARS-CoV-2 antibody inhibits variants of concern by utilizing unique binding residues in a highly conserved epitope.

VanBlargan, Laura A; Adams, Lucas J; Liu, Zhuoming; Chen, Rita E; Gilchuk, Pavlo; Raju, Saravanan; Smith, Brittany K; Zhao, Haiyan; Case, James Brett; Winkler, Emma S; Whitener, Bradley M; Droit, Lindsay; Aziati, Ishmael D; Bricker, Traci L; Joshi, Astha; Shi, Pei-Yong; Creanga, Adrian; Pegu, Amarendra; Handley, Scott A; Wang, David; Boon, Adrianus C M; Crowe, James E; Whelan, Sean P J; Fremont, Daved H; Diamond, Michael S.

Immunity ; 54(10): 2399-2416.e6, 2021 10 12.

Artículo en Inglés | MEDLINE | ID: mdl-34481543

4.

Disease-specific alterations in the enteric virome in inflammatory bowel disease.

Norman, Jason M; Handley, Scott A; Baldridge, Megan T; Droit, Lindsay; Liu, Catherine Y; Keller, Brian C; Kambal, Amal; Monaco, Cynthia L; Zhao, Guoyan; Fleshner, Phillip; Stappenbeck, Thaddeus S; McGovern, Dermot P B; Keshavarzian, Ali; Mutlu, Ece A; Sauk, Jenny; Gevers, Dirk; Xavier, Ramnik J; Wang, David; Parkes, Miles; Virgin, Herbert W.

Cell ; 160(3): 447-60, 2015 Jan 29.

Artículo en Inglés | MEDLINE | ID: mdl-25619688

5.

Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome.

Handley, Scott A; Thackray, Larissa B; Zhao, Guoyan; Presti, Rachel; Miller, Andrew D; Droit, Lindsay; Abbink, Peter; Maxfield, Lori F; Kambal, Amal; Duan, Erning; Stanley, Kelly; Kramer, Joshua; Macri, Sheila C; Permar, Sallie R; Schmitz, Joern E; Mansfield, Keith; Brenchley, Jason M; Veazey, Ronald S; Stappenbeck, Thaddeus S; Wang, David; Barouch, Dan H; Virgin, Herbert W.

Cell ; 151(2): 253-66, 2012 Oct 12.

Artículo en Inglés | MEDLINE | ID: mdl-23063120

6.

In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains.

Chen, Rita E; Winkler, Emma S; Case, James Brett; Aziati, Ishmael D; Bricker, Traci L; Joshi, Astha; Darling, Tamarand L; Ying, Baoling; Errico, John M; Shrihari, Swathi; VanBlargan, Laura A; Xie, Xuping; Gilchuk, Pavlo; Zost, Seth J; Droit, Lindsay; Liu, Zhuoming; Stumpf, Spencer; Wang, David; Handley, Scott A; Stine, W Blaine; Shi, Pei-Yong; Davis-Gardner, Meredith E; Suthar, Mehul S; Knight, Miguel Garcia; Andino, Raul; Chiu, Charles Y; Ellebedy, Ali H; Fremont, Daved H; Whelan, Sean P J; Crowe, James E; Purcell, Lisa; Corti, Davide; Boon, Adrianus C M; Diamond, Michael S.

Nature ; 596(7870): 103-108, 2021 08.

Artículo en Inglés | MEDLINE | ID: mdl-34153975

7.

Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women.

Gosmann, Christina; Anahtar, Melis N; Handley, Scott A; Farcasanu, Mara; Abu-Ali, Galeb; Bowman, Brittany A; Padavattan, Nikita; Desai, Chandni; Droit, Lindsay; Moodley, Amber; Dong, Mary; Chen, Yuezhou; Ismail, Nasreen; Ndung'u, Thumbi; Ghebremichael, Musie S; Wesemann, Duane R; Mitchell, Caroline; Dong, Krista L; Huttenhower, Curtis; Walker, Bruce D; Virgin, Herbert W; Kwon, Douglas S.

Immunity ; 46(1): 29-37, 2017 01 17.

Artículo en Inglés | MEDLINE | ID: mdl-28087240

8.

The Highly Conserved Stem-Loop II Motif Is Dispensable for SARS-CoV-2.

Jiang, Hongbing; Joshi, Astha; Gan, Tianyu; Janowski, Andrew B; Fujii, Chika; Bricker, Traci L; Darling, Tamarand L; Harastani, Houda H; Seehra, Kuljeet; Chen, Hongwei; Tahan, Stephen; Jung, Ana; Febles, Binita; Blatter, Joshua A; Handley, Scott A; Parikh, Bijal A; Wang, David; Boon, Adrianus C M.

J Virol ; 97(6): e0063523, 2023 06 29.

Artículo en Inglés | MEDLINE | ID: mdl-37223945

9.

UFMylation inhibits the proinflammatory capacity of interferon-Î³-activated macrophages.

Balce, Dale R; Wang, Ya-Ting; McAllaster, Michael R; Dunlap, Bria F; Orvedahl, Anthony; Hykes, Barry L; Droit, Lindsay; Handley, Scott A; Wilen, Craig B; Doench, John G; Orchard, Robert C; Stallings, Christina L; Virgin, Herbert W.

Proc Natl Acad Sci U S A ; 118(1)2021 01 05.

Artículo en Inglés | MEDLINE | ID: mdl-33372156

10.

Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome.

Mihindukulasuriya, Kathie A; Mars, Ruben A T; Johnson, Abigail J; Ward, Tonya; Priya, Sambhawa; Lekatz, Heather R; Kalari, Krishna R; Droit, Lindsay; Zheng, Tenghao; Blekhman, Ran; D'Amato, Mauro; Farrugia, Gianrico; Knights, Dan; Handley, Scott A; Kashyap, Purna C.

Gastroenterology ; 161(4): 1194-1207.e8, 2021 10.

Artículo en Inglés | MEDLINE | ID: mdl-34245762

11.

Autophagy genes in myeloid cells counteract IFNÎ³-induced TNF-mediated cell death and fatal TNF-induced shock.

Orvedahl, Anthony; McAllaster, Michael R; Sansone, Amy; Dunlap, Bria F; Desai, Chandni; Wang, Ya-Ting; Balce, Dale R; Luke, Cliff J; Lee, Sanghyun; Orchard, Robert C; Artyomov, Maxim N; Handley, Scott A; Doench, John G; Silverman, Gary A; Virgin, Herbert W.

Proc Natl Acad Sci U S A ; 116(33): 16497-16506, 2019 08 13.

Artículo en Inglés | MEDLINE | ID: mdl-31346084

12.

Sex effects in the association between airway microbiome and asthma.

Chen, Renjin; Wang, Leran; Koch, Tammy; Curtis, Vanessa; Yin-DeClue, Huiqing; Handley, Scott A; Shan, Liang; Holtzman, Michael J; Castro, Mario; Wang, Leyao.

Ann Allergy Asthma Immunol ; 125(6): 652-657.e3, 2020 12.

Artículo en Inglés | MEDLINE | ID: mdl-32931909

13.

LysMD3 is a type II membrane protein without an in vivo role in the response to a range of pathogens.

Yokoyama, Christine C; Baldridge, Megan T; Leung, Daisy W; Zhao, Guoyan; Desai, Chandni; Liu, Ta-Chiang; Diaz-Ochoa, Vladimir E; Huynh, Jeremy P; Kimmey, Jacqueline M; Sennott, Erica L; Hole, Camaron R; Idol, Rachel A; Park, Sunmin; Storek, Kelly M; Wang, Caihong; Hwang, Seungmin; Viehmann Milam, Ashley; Chen, Eric; Kerrinnes, Tobias; Starnbach, Michael N; Handley, Scott A; Mysorekar, Indira U; Allen, Paul M; Monack, Denise M; Dinauer, Mary C; Doering, Tamara L; Tsolis, Renee M; Dworkin, Jonathan E; Stallings, Christina L; Amarasinghe, Gaya K; Micchelli, Craig A; Virgin, Herbert W.

J Biol Chem ; 293(16): 6022-6038, 2018 04 20.

Artículo en Inglés | MEDLINE | ID: mdl-29496999

14.

Ten simple rules and a template for creating workflows-as-applications.

Roach, Michael J; Pierce-Ward, N Tessa; Suchecki, Radoslaw; Mallawaarachchi, Vijini; Papudeshi, Bhavya; Handley, Scott A; Brown, C Titus; Watson-Haigh, Nathan S; Edwards, Robert A.

PLoS Comput Biol ; 18(12): e1010705, 2022 12.

Artículo en Inglés | MEDLINE | ID: mdl-36520686

15.

Construction and evaluation of novel rhesus monkey adenovirus vaccine vectors.

Abbink, Peter; Maxfield, Lori F; Ng'ang'a, David; Borducchi, Erica N; Iampietro, M Justin; Bricault, Christine A; Teigler, Jeffrey E; Blackmore, Stephen; Parenteau, Lily; Wagh, Kshitij; Handley, Scott A; Zhao, Guoyan; Virgin, Herbert W; Korber, Bette; Barouch, Dan H.

J Virol ; 89(3): 1512-22, 2015 Feb.

Artículo en Inglés | MEDLINE | ID: mdl-25410856

16.

Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities.

Norman, Jason M; Handley, Scott A; Virgin, Herbert W.

Gastroenterology ; 146(6): 1459-69, 2014 May.

Artículo en Inglés | MEDLINE | ID: mdl-24508599

17.

Draft genomes of 12 Bifidobacterium isolates from human IBD fecal samples.

Souza, Cole E; Jacobson, Nicole E; An, Michelle A; Droit, Lindsay; Vega, Alejandro A; Rosales, Mariel; Mihindukulasuriya, Kathie A; Pastrana, Karina; Handley, Scott A; Parkes, Miles; Rimmer, Joanna; Wang, David; Dinsdale, Elizabeth A; A Edwards, Robert; Segall, Anca M.

Microbiol Resour Announc ; 13(1): e0013023, 2024 Jan 17.

Artículo en Inglés | MEDLINE | ID: mdl-38099679

18.

HIV-associated gut microbial alterations are dependent on host and geographic context.

Rocafort, Muntsa; Gootenberg, David B; Luévano, Jesús M; Paer, Jeffrey M; Hayward, Matthew R; Bramante, Juliet T; Ghebremichael, Musie S; Xu, Jiawu; Rogers, Zoe H; Munoz, Alexander R; Okello, Samson; Kim, June-Ho; Sentongo, Ruth; Wagubi, Robert; Lankowski, Alex; Maruapula, Segametsi; Zhao, Guoyan; Handley, Scott A; Mosepele, Mosepele; Siedner, Mark J; Kwon, Douglas S.

Nat Commun ; 15(1): 1055, 2024 Feb 05.

Artículo en Inglés | MEDLINE | ID: mdl-38316748

19.

The history and organization of the Workshop on Population and Speciation Genomics.

Barth, Julia M I; Handley, Scott A; Kintzl, Daniel; Leonard, Guy; Malinsky, Milan; Matschiner, Michael; Meyer, Britta S; Salzburger, Walter; Stefka, Jan; Trucchi, Emiliano.

Evolution (N Y) ; 16(1): 2, 2023.

Artículo en Inglés | MEDLINE | ID: mdl-36789285

20.

Tracking the prevalence and emergence of SARS CoV2 variants of concern using a regional genomic surveillance program.

Jung, Ana; Droit, Lindsay; Febles, Binita; Fronick, Catarina; Cook, Lisa; Handley, Scott A; Parikh, Bijal A; Wang, David.

medRxiv ; 2023 May 10.

Artículo en Inglés | MEDLINE | ID: mdl-37214888

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