S Banakis

Affiliations

Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH , Bethesda, Maryland, USA.

Publications (13)

Microbial signatures in the lower airways of mechanically ventilated COVID19 patients associated with poor clinical outcome.

medRxiv : the preprint server for health sciences

Avec: Imran Sulaiman , Matthew Chung , Luis Angel , Jun-Chieh J Tsay , Benjamin G Wu , Stephen T Yeung , Kelsey Krolikowski , Yonghua Li , Ralf Duerr , Rosemary Schluger , Sara A Thannickal , Akiko Koide , Samaan Rafeq , Clea Barnett , Radu Postelnicu , Chang Wang , Stephanie Banakis , Lizzette Perez-Perez , George Jour , Guomiao Shen , Peter Meyn , Joseph Carpenito , Xiuxiu Liu , Kun Ji , Destiny Collazo , Anthony Labarbiera , Nancy Amoroso , Shari Brosnahan , Vikramjit Mukherjee , David Kaufman , Jan Bakker , Anthony Lubinsky , Deepak Pradhan , Daniel H Sterman , Michael Weiden , Adriana Hegu , Laura Evans , Timothy M Uyeki , Jose C Clemente , Emmie De Wit , Ann Marie Schmidt , Bo Shopsin , Ludovic Desvignes , Chan Wang , Huilin Li , Bin Zhang , Christian V Forst , Shohei Koide , Kenneth A Stapleford , Kamal M Khanna , Elodie Ghedin , Leopoldo N Segal

Microbial signatures in the lower airways of mechanically ventilated COVID19 patients associated with poor clinical outcome.

Research square

Avec: Imran Sulaiman , Matthew Chung , Luis Angel , Sergei Koralov , Benjamin Wu , Stephen Yeung , Kelsey Krolikowski , Yonghua Li , Ralf Duerr , Rosemary Schluger , Sara Thannickal , Akiko Koide , Samaan Rafeq , Clea Barnett , Radu Postelnicu , Chang Wang , Stephanie Banakis , Lizzette Perez-Perez , George Jour , Guomiao Shen , Peter Meyn , Joseph Carpenito , Xiuxiu Liu , Kun Ji , Destiny Collazo , Anthony Labarbiera , Nancy Amoroso , Shari Brosnahan , Vikramjit Mukherjee , David Kaufman , Jan Bakker , Anthony Lubinsky , Deepak Pradhan , Daniel Sterman , Adriana Heguy , Timothy Uyeki , Jose Clemente , Emmie de Wit , Ann Marie Schmidt , Bo Shopsin , Ludovic Desvignes , Chan Wang , Huilin Li , Bin Zhang , Christian Forst , Shohei Koide , Kenneth Stapleford , Kamal Khanna , Elodie Ghedin , Michael Weiden , Leopoldo Segal

CD4+ and CD8+ T cells are required to prevent SARS-CoV-2 persistence in the nasal compartment.

bioRxiv : the preprint server for biology

Avec: Meenakshi Kar , Katherine E E Johnson , Abigail Vanderheiden , Elizabeth J Elrod , Katharine Floyd , Elizabeth Geerling , E Taylor Stone , Eduardo Salinas , Stephanie Banakis , Wei Wang , Shruti Sathish , Swathi Shrihari , Meredith E Davis-Gardner , Jacob Kohlmeier , Amelia Pinto , Robyn Klein , Arash Grakoui , Elodie Ghedin , Mehul S Suthar

Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion.

medRxiv : the preprint server for health sciences

Avec: Veronique Nussenblatt , Allison E Roder , Sanchita Das , Emmie de Wit , Jung-Ho Youn , Stephanie Banakis , Alexandra Mushegian , Christopher Mederos , Wei Wang , Matthew Chung , Lizzette Pérez-Pérez , Tara Palmore , Jennifer N Brudno , James N Kochenderfer , Elodie Ghedin

Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections.

medRxiv : the preprint server for health sciences

Avec: Mohammed Nooruzzaman , Katherine E E Johnson , Ruchi Rani , Eli J Finkelsztein , Leonardo C Caserta , Rosy P Kodiyanplakkal , Wei Wang , Jingmei Hsu , Maria T Salpietro , Stephanie Banakis , Joshua Albert , Lars Westblade , Claudio Zanettini , Luigi Marchionni , Rosemary Soave , Elodie Ghedin , Diego G Diel , Mirella Salvatore

Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections.

Nature communications

Avec: Mohammed Nooruzzaman , Katherine E E Johnson , Ruchi Rani , Eli J Finkelsztein , Leonardo C Caserta , Rosy P Kodiyanplakkal , Wei Wang , Jingmei Hsu , Maria T Salpietro , Stephanie Banakis , Joshua Albert , Lars F Westblade , Claudio Zanettini , Luigi Marchionni , Rosemary Soave , Elodie Ghedin , Diego G Diel , Mirella Salvatore

Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism.

The European respiratory journal

Avec: Imran Sulaiman , Benjamin G Wu , Yonghua Li , Jun-Chieh Tsay , Maya Sauthoff , Adrienne S Scott , Kun Ji , Sergei B Koralov , Michael Weiden , Jose C Clemente , Drew Jones , Yvonne J Huang , Kathleen A Stringer , Lingdi Zhang , Adam Geber , Stephanie Banakis , Laura Tipton , Elodie Ghedin , Leopoldo N Segal

CD4

Science advances

Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data.

mBio

Avec: A E Roder , K E E Johnson , M Knoll , M Khalfan , B Wang , S Schultz-Cherry , S Banakis , A Kreitman , C Mederos , J-H Youn , R Mercado , W Wang , M Chung , D Ruchnewitz , M I Samanovic , M J Mulligan , M Lässig , M Luksza , S Das , D Gresham , E Ghedin

Yearlong COVID-19 Infection Reveals Within-Host Evolution of SARS-CoV-2 in a Patient With B-Cell Depletion.

The Journal of infectious diseases

Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome.

Nature microbiology

Avec: Imran Sulaiman , Matthew Chung , Luis Angel , Jun-Chieh J Tsay , Benjamin G Wu , Stephen T Yeung , Kelsey Krolikowski , Yonghua Li , Ralf Duerr , Rosemary Schluger , Sara A Thannickal , Akiko Koide , Samaan Rafeq , Clea Barnett , Radu Postelnicu , Chang Wang , Stephanie Banakis , Lizzette Pérez-Pérez , Guomiao Shen , George Jour , Peter Meyn , Joseph Carpenito , Xiuxiu Liu , Kun Ji , Destiny Collazo , Anthony Labarbiera , Nancy Amoroso , Shari Brosnahan , Vikramjit Mukherjee , David Kaufman , Jan Bakker , Anthony Lubinsky , Deepak Pradhan , Daniel H Sterman , Michael Weiden , Adriana Heguy , Laura Evans , Timothy M Uyeki , Jose C Clemente , Emmie de Wit , Ann Marie Schmidt , Bo Shopsin , Ludovic Desvignes , Chan Wang , Huilin Li , Bin Zhang , Christian V Forst , Shohei Koide , Kenneth A Stapleford , Kamal M Khanna , Elodie Ghedin , Leopoldo N Segal

Successful lung transplantation using an allograft from a COVID-19-recovered donor: a potential role for subgenomic RNA to guide organ utilization.

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons

Avec: Kapil K Saharia , Sabrina C Ramelli , Sydney R Stein , Allison E Roder , Allie Kreitman , Stephanie Banakis , Joon-Yong Chung , Peter D Burbelo , Manmeet Singh , Robert M Reed , Vipul Patel , Joseph Rabin , Alexander S Krupnick , Jeffrey I Cohen , Emmie de Wit , Elodie Ghedin , Stephen M Hewitt , Kevin M Vannella , Daniel S Chertow , Alison Grazioli

Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data.

bioRxiv : the preprint server for biology

Avec: A E Roder , Kee Johnson , M Knoll , M Khalfan , B Wang , S Schultz-Cherry , S Banakis , A Kreitman , C Mederos , J-H Youn , R Mercado , W Wang , D Ruchnewitz , M I Samanovic , M J Mulligan , M Lassig , M Åuksza , S Das , D Gresham , E Ghedin

Réseau de co-auteurs

Stephanie Banakis 11 collaborations

Elodie Ghedin 11 collaborations

Wei Wang 6 collaborations

Matthew Chung 5 collaborations

Emmie de Wit 5 collaborations

Imran Sulaiman 4 collaborations

Yonghua Li 4 collaborations

Kun Ji 4 collaborations

Michael Weiden 4 collaborations

Katherine E E Johnson 4 collaborations

Luis Angel 3 collaborations

Benjamin G Wu 3 collaborations

Kelsey Krolikowski 3 collaborations

Ralf Duerr 3 collaborations

Rosemary Schluger 3 collaborations

Akiko Koide 3 collaborations

Samaan Rafeq 3 collaborations

Clea Barnett 3 collaborations

Radu Postelnicu 3 collaborations

Chang Wang 3 collaborations

George Jour 3 collaborations

Guomiao Shen 3 collaborations

Peter Meyn 3 collaborations

Joseph Carpenito 3 collaborations

Xiuxiu Liu 3 collaborations

Destiny Collazo 3 collaborations

Anthony Labarbiera 3 collaborations

Nancy Amoroso 3 collaborations

Shari Brosnahan 3 collaborations

Vikramjit Mukherjee 3 collaborations

David Kaufman 3 collaborations

Jan Bakker 3 collaborations

Anthony Lubinsky 3 collaborations

Deepak Pradhan 3 collaborations

Jose C Clemente 3 collaborations

Ann Marie Schmidt 3 collaborations

Bo Shopsin 3 collaborations

Ludovic Desvignes 3 collaborations

Chan Wang 3 collaborations

Huilin Li 3 collaborations

Bin Zhang 3 collaborations

Shohei Koide 3 collaborations

Leopoldo N Segal 3 collaborations

Allison E Roder 3 collaborations

Lizzette Pérez-Pérez 3 collaborations

Jun-Chieh J Tsay 2 collaborations

Stephen T Yeung 2 collaborations

Sara A Thannickal 2 collaborations

Lizzette Perez-Perez 2 collaborations

Daniel H Sterman 2 collaborations

Laura Evans 2 collaborations

Timothy M Uyeki 2 collaborations

Christian V Forst 2 collaborations

Kenneth A Stapleford 2 collaborations

Kamal M Khanna 2 collaborations

Adriana Heguy 2 collaborations

Meenakshi Kar 2 collaborations

Abigail Vanderheiden 2 collaborations

Elizabeth J Elrod 2 collaborations

Katharine Floyd 2 collaborations

Elizabeth Geerling 2 collaborations

E Taylor Stone 2 collaborations

Eduardo Salinas 2 collaborations

Shruti Sathish 2 collaborations

Swathi Shrihari 2 collaborations

Meredith E Davis-Gardner 2 collaborations

Jacob Kohlmeier 2 collaborations

Amelia Pinto 2 collaborations

Robyn Klein 2 collaborations

Arash Grakoui 2 collaborations

Mehul S Suthar 2 collaborations

Veronique Nussenblatt 2 collaborations

Sanchita Das 2 collaborations

Jung-Ho Youn 2 collaborations

Alexandra Mushegian 2 collaborations

Christopher Mederos 2 collaborations

Tara Palmore 2 collaborations

Jennifer N Brudno 2 collaborations

James N Kochenderfer 2 collaborations

Mohammed Nooruzzaman 2 collaborations

Ruchi Rani 2 collaborations

Eli J Finkelsztein 2 collaborations

Leonardo C Caserta 2 collaborations

Rosy P Kodiyanplakkal 2 collaborations

Jingmei Hsu 2 collaborations

Maria T Salpietro 2 collaborations

Joshua Albert 2 collaborations

Claudio Zanettini 2 collaborations

Luigi Marchionni 2 collaborations

Rosemary Soave 2 collaborations

Diego G Diel 2 collaborations

Mirella Salvatore 2 collaborations

A E Roder 2 collaborations

M Knoll 2 collaborations

M Khalfan 2 collaborations

B Wang 2 collaborations

S Schultz-Cherry 2 collaborations

A Kreitman 2 collaborations

C Mederos 2 collaborations

J-H Youn 2 collaborations

R Mercado 2 collaborations

W Wang 2 collaborations

D Ruchnewitz 2 collaborations

M I Samanovic 2 collaborations

M J Mulligan 2 collaborations

S Das 2 collaborations

D Gresham 2 collaborations

E Ghedin 2 collaborations

Adriana Hegu 1 collaboration

Emmie De Wit 1 collaboration

Sergei Koralov 1 collaboration

Benjamin Wu 1 collaboration

Stephen Yeung 1 collaboration

Sara Thannickal 1 collaboration

Daniel Sterman 1 collaboration

Timothy Uyeki 1 collaboration

Jose Clemente 1 collaboration

Christian Forst 1 collaboration

Kenneth Stapleford 1 collaboration

Kamal Khanna 1 collaboration

Leopoldo Segal 1 collaboration

Lars Westblade 1 collaboration

Lars F Westblade 1 collaboration

Jun-Chieh Tsay 1 collaboration

Maya Sauthoff 1 collaboration

Adrienne S Scott 1 collaboration

Sergei B Koralov 1 collaboration

Drew Jones 1 collaboration

Yvonne J Huang 1 collaboration

Kathleen A Stringer 1 collaboration

Lingdi Zhang 1 collaboration

Adam Geber 1 collaboration

Laura Tipton 1 collaboration

K E E Johnson 1 collaboration

M Chung 1 collaboration

M Lässig 1 collaboration

M Luksza 1 collaboration

Kapil K Saharia 1 collaboration

Sabrina C Ramelli 1 collaboration

Sydney R Stein 1 collaboration

Allie Kreitman 1 collaboration

Joon-Yong Chung 1 collaboration

Peter D Burbelo 1 collaboration

Manmeet Singh 1 collaboration

Robert M Reed 1 collaboration

Vipul Patel 1 collaboration

Joseph Rabin 1 collaboration

Alexander S Krupnick 1 collaboration

Jeffrey I Cohen 1 collaboration

Stephen M Hewitt 1 collaboration

Kevin M Vannella 1 collaboration

Daniel S Chertow 1 collaboration

Alison Grazioli 1 collaboration

Kee Johnson 1 collaboration

M Lassig 1 collaboration

M Åuksza 1 collaboration