Recent Publications
- Enhancing scientific discoveries in molecular biology with deep generative models.
Lopez R, Gayoso A, Yosef N
Molecular systems biology. 2020 Sep
PMID: 32975352
- Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2.
Wyllie 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
The New England journal of medicine. 2020 Sep 24
PMID: 32857487
- Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models.
Xu C, Lopez R, Mehlman E, Regier J, Jordan MI, Yosef N
Molecular systems biology. 2021 Jan
PMID: 33491336
- Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant.
Edara VV, Norwood C, Floyd K, Lai L, Davis-Gardner ME, Hudson WH, Mantus G, Nyhoff LE, Adelman MW, Fineman R, Patel S, Byram R, Gomes DN, Michael G, Abdullahi H, Beydoun N, Panganiban B, McNair N, Hellmeister K, Pitts J, Winters J, Kleinhenz J, Usher J, O'Keefe JB, Piantadosi A, Waggoner JJ, Babiker A, Stephens DS, Anderson EJ, Edupuganti S, Rouphael N, Ahmed R, Wrammert J, Suthar MS
Cell host & microbe. 2021 Mar 20
PMID: 33798491
- Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes.
Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, Niklason LE, Montgomery RR, Eisenbarth SC, Chen S, Williams A, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, Pyle AM, van Dijk D, Wilen CB
PLoS biology. 2021 Mar
PMID: 33730024
- Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts.
Quinn JJ, Jones MG, Okimoto RA, Nanjo S, Chan MM, Yosef N, Bivona TG, Weissman JS
Science (New York, N.Y.). 2021 Feb 26
PMID: 33479121
- Longitudinal shear stress response in human endothelial cells to atheroprone and atheroprotective conditions.
Maurya MR, Gupta S, Li JY, Ajami NE, Chen ZB, Shyy JY, Chien S, Subramaniam S
Proceedings of the National Academy of Sciences of the United States of America. 2021 Jan 26
PMID: 33468662
- JAK-inhibitor and type I interferon ability to produce favorable clinical outcomes in COVID-19 patients: a systematic review and meta-analysis.
Walz L, Cohen AJ, Rebaza AP, Vanchieri J, Slade MD, Dela Cruz CS, Sharma L
BMC infectious diseases. 2021 Jan 11
PMID: 33430799
- Comprehensive analysis of COVID-19 during pregnancy.
Moore KM, Suthar MS
Biochemical and biophysical research communications. 2021 Jan 29
PMID: 33384142
- Mass Cytometry Defines Virus-Specific CD4+ T Cells in Influenza Vaccination.
Subrahmanyam PB, Holmes TH, Lin D, Su LF, Obermoser G, Banchereau J, Pascual V, García-Sastre A, Albrecht RA, Palucka K, Davis MM, Maecker HT
ImmunoHorizons. 2020 Dec 11
PMID: 33310880
- In-Depth Analysis of Genetic Variation Associated with Severe West Nile Viral Disease.
Cahill ME, Loeb M, Dewan AT, Montgomery RR
Vaccines. 2020 Dec 8
PMID: 33302579
- The immunology of SARS-CoV-2 infections and vaccines.
Grigoryan L, Pulendran B
Seminars in immunology. 2020 Aug
PMID: 33262067
- Development of a Rapid Focus Reduction Neutralization Test Assay for Measuring SARS-CoV-2 Neutralizing Antibodies.
Vanderheiden A, Edara VV, Floyd K, Kauffman RC, Mantus G, Anderson E, Rouphael N, Edupuganti S, Shi PY, Menachery VD, Wrammert J, Suthar MS
Current protocols in immunology. 2020 Dec
PMID: 33215858
- Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis.
Pompura SL, Wagner A, Kitz A, LaPerche J, Yosef N, Dominguez-Villar M, Hafler DA
The Journal of clinical investigation. 2021 Jan 19
PMID: 33170805
- Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells.
Sumida TS, Dulberg S, Schupp J, Stillwell HA, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA
bioRxiv : the preprint server for biology. 2020 Oct 31
PMID: 33140047
- Epigenetic fine-mapping: identification of causal mechanisms for autoimmunity.
Lincoln MR, Axisa PP, Hafler DA
Current opinion in immunology. 2020 Dec
PMID: 32977183
- Innate Lymphoid Cell Activation and Sustained Depletion in Blood and Tissue of Children Infected with HIV from Birth Despite Antiretroviral Therapy.
Singh A, Kazer SW, Roider J, Krista KC, Millar J, Asowata OE, Ngoepe A, Ramsuran D, Fardoos R, Ardain A, Muenchhoff M, Kuhn W, Karim F, Ndung'u T, Shalek AK, Goulder P, Leslie A, Kløverpris HN
Cell reports. 2020 Sep 15
PMID: 32937142
- JAK-Inhibitor and Type I Interferon Ability to Produce Favorable Clinical Outcomes in COVID-19 Patients: A Systematic Review and Meta-Analysis.
Walz L, Cohen AJ, Rebaza AP, Vanchieri J, Slade MD, Dela Cruz CS, Sharma L
Research square. 2020 Aug 26
PMID: 32869016
- Janus Kinase-Inhibitor and Type I Interferon Ability to Produce Favorable Clinical Outcomes in COVID-19 Patients: A Systematic Review and Meta-Analysis.
Walz L, Cohen AJ, Rebaza AP, Vanchieri J, Slade MD, Dela Cruz CS, Sharma L
medRxiv : the preprint server for health sciences. 2020 Aug 11
PMID: 32817985
- Severe SARS-CoV-2 infection in humans is defined by a shift in the serum lipidome resulting in dysregulation of eicosanoid immune mediators.
Schwarz B, Sharma L, Roberts L, Peng X, Bermejo S, Leighton I, Massana AC, Farhadian S, Ko AI, Yale IMPACT Team., Cruz CSD, Bosio CM
Research square. 2020 Jul 22
PMID: 32743565
- AgBR1 and NeSt1 antisera protect mice from Aedes aegypti-borne Zika infection.
Marin-Lopez A, Wang Y, Jiang J, Ledizet M, Fikrig E
Vaccine. 2021 Mar 19
PMID: 33622591
- The Impact of the Microbiome on Immunity to Vaccination in Humans.
de Jong SE, Olin A, Pulendran B
Cell host & microbe. 2020 Aug 12
PMID: 32791110
- Antigenicity prediction and vaccine recommendation of human influenza virus A (H3N2) using convolutional neural networks.
Lee EK, Tian H, Nakaya HI
Human vaccines & immunotherapeutics. 2020 Nov 1
PMID: 32750260
- Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans.
Arunachalam PS, Wimmers F, Mok CKP, Perera RAPM, Scott M, Hagan T, Sigal N, Feng Y, Bristow L, Tak-Yin Tsang O, Wagh D, Coller J, Pellegrini KL, Kazmin D, Alaaeddine G, Leung WS, Chan JMC, Chik TSH, Choi CYC, Huerta C, Paine McCullough M, Lv H, Anderson E, Edupuganti S, Upadhyay AA, Bosinger SE, Maecker HT, Khatri P, Rouphael N, Peiris M, Pulendran B
Science (New York, N.Y.). 2020 Sep 4
PMID: 32788292
- Cutting Edge: Severe SARS-CoV-2 Infection in Humans Is Defined by a Shift in the Serum Lipidome, Resulting in Dysregulation of Eicosanoid Immune Mediators.
Schwarz B, Sharma L, Roberts L, Peng X, Bermejo S, Leighton I, Casanovas-Massana A, Minasyan M, Farhadian S, Ko AI, Yale IMPACT Team., Dela Cruz CS, Bosio CM
Journal of immunology (Baltimore, Md. : 1950). 2021 Jan 15
PMID: 33277388
- Human germinal centres engage memory and naive B cells after influenza vaccination.
Turner JS, Zhou JQ, Han J, Schmitz AJ, Rizk AA, Alsoussi WB, Lei T, Amor M, McIntire KM, Meade P, Strohmeier S, Brent RI, Richey ST, Haile A, Yang YR, Klebert MK, Suessen T, Teefey S, Presti RM, Krammer F, Kleinstein SH, Ward AB, Ellebedy AH
Nature. 2020 Oct
PMID: 32866963
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