Recent Publications
- Recovering Gene Interactions from Single-Cell Data Using Data Diffusion.
van Dijk D, Sharma R, Nainys J, Yim K, Kathail P, Carr AJ, Burdziak C, Moon KR, Chaffer CL, Pattabiraman D, Bierie B, Mazutis L, Wolf G, Krishnaswamy S, Pe'er D
Cell. 2018 Jul 26
PMID: 29961576
- Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging.
Cheung P, Vallania F, Warsinske HC, Donato M, Schaffert S, Chang SE, Dvorak M, Dekker CL, Davis MM, Utz PJ, Khatri P, Kuo AJ
Cell. 2018 May 31
PMID: 29706550
- The Neurocognitive and MRI Outcomes of West Nile Virus Infection: Preliminary Analysis Using an External Control Group.
Murray KO, Nolan MS, Ronca SE, Datta S, Govindarajan K, Narayana PA, Salazar L, Woods SP, Hasbun R
Frontiers in neurology. 2018
PMID: 29636722
- Varicella-Zoster Virus DNA in Blood After Administration of Herpes Zoster Vaccine.
Levin MJ, Cai GY, Lee KS, Rouphael NG, Mehta AK, Canniff J, Mulligan MJ, Weinberg A
The Journal of infectious diseases. 2018 Mar 13
PMID: 29409017
- A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers.
Martin-Gayo E, Cole MB, Kolb KE, Ouyang Z, Cronin J, Kazer SW, Ordovas-Montanes J, Lichterfeld M, Walker BD, Yosef N, Shalek AK, Yu XG
Genome biology. 2018 Jan 29
PMID: 29378643
- Transcriptomic signatures of cellular and humoral immune responses in older adults after seasonal influenza vaccination identified by data-driven clustering.
Voigt EA, Grill DE, Zimmermann MT, Simon WL, Ovsyannikova IG, Kennedy RB, Poland GA
Scientific reports. 2018 Jan 15
PMID: 29335477
- Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.
Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ
Nature biotechnology. 2018 Jan
PMID: 29227470
- Identification of genetic variants associated with dengue or West Nile virus disease: a systematic review and meta-analysis.
Cahill ME, Conley S, DeWan AT, Montgomery RR
BMC infectious diseases. 2018 Jun 22
PMID: 29929468
- RAF/MEK/extracellular signal-related kinase pathway suppresses dendritic cell migration and traps dendritic cells in Langerhans cell histiocytosis lesions.
Hogstad B, Berres ML, Chakraborty R, Tang J, Bigenwald C, Serasinghe M, Lim KPH, Lin H, Man TK, Remark R, Baxter S, Kana V, Jordan S, Karoulia Z, Kwan WH, Leboeuf M, Brandt E, Salmon H, McClain K, Poulikakos P, Chipuk J, Mulder WJM, Allen CE, Merad M
The Journal of experimental medicine. 2018 Jan 2
PMID: 29263218
- A multidimensional blood stimulation assay reveals immune alterations underlying systemic juvenile idiopathic arthritis.
Cepika AM, Banchereau R, Segura E, Ohouo M, Cantarel B, Goller K, Cantrell V, Ruchaud E, Gatewood E, Nguyen P, Gu J, Anguiano E, Zurawski S, Baisch JM, Punaro M, Baldwin N, Obermoser G, Palucka K, Banchereau J, Amigorena S, Pascual V
The Journal of experimental medicine. 2017 Nov 6
PMID: 28935693
- Co-expression Network Approach Reveals Functional Similarities among Diseases Affecting Human Skeletal Muscle.
Mukund K, Subramaniam S
Frontiers in physiology. 2017
PMID: 29249983
- Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? From Data to Understanding through Systems Biology.
Hagan T, Pulendran B
Cold Spring Harbor perspectives in biology. 2017 Oct 16
PMID: 29038113
- Age-related changes in expression and signaling of TAM receptor inflammatory regulators in monocytes.
Wang X, Malawista A, Qian F, Ramsey C, Allore HG, Montgomery RR
Oncotarget. 2018 Feb 9
PMID: 29515754
- Multiple network-constrained regressions expand insights into influenza vaccination responses.
Avey S, Mohanty S, Wilson J, Zapata H, Joshi SR, Siconolfi B, Tsang S, Shaw AC, Kleinstein SH
Bioinformatics (Oxford, England). 2017 Jul 15
PMID: 28881994
- Single-cell analyses to tailor treatments.
Shalek AK, Benson M
Science translational medicine. 2017 Sep 20
PMID: 28931656
- Taking the defensive: Immune control of Zika virus infection.
Bowen JR, Zimmerman MG, Suthar MS
Virus research. 2017 Sep 1
PMID: 28867493
- KLRD1-expressing natural killer cells predict influenza susceptibility.
Bongen E, Vallania F, Utz PJ, Khatri P
Genome medicine. 2018 Jun 14
PMID: 29898768
- Aging impairs both primary and secondary RIG-I signaling for interferon induction in human monocytes.
Molony RD, Nguyen JT, Kong Y, Montgomery RR, Shaw AC, Iwasaki A
Science signaling. 2017 Dec 12
PMID: 29233916
- Humanized mouse model supports development, function, and tissue residency of human natural killer cells.
Herndler-Brandstetter D, Shan L, Yao Y, Stecher C, Plajer V, Lietzenmayer M, Strowig T, de Zoete MR, Palm NW, Chen J, Blish CA, Frleta D, Gurer C, Macdonald LE, Murphy AJ, Yancopoulos GD, Montgomery RR, Flavell RA
Proceedings of the National Academy of Sciences of the United States of America. 2017 Nov 7
PMID: 29078283
- Systems biology analysis of longitudinal functional response of endothelial cells to shear stress.
Ajami NE, Gupta S, Maurya MR, Nguyen P, Li JY, Shyy JY, Chen Z, Chien S, Subramaniam S
Proceedings of the National Academy of Sciences of the United States of America. 2017 Oct 10
PMID: 28973892
- BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.
Upadhyay AA, Kauffman RC, Wolabaugh AN, Cho A, Patel NB, Reiss SM, Havenar-Daughton C, Dawoud RA, Tharp GK, Sanz I, Pulendran B, Crotty S, Lee FE, Wrammert J, Bosinger SE
Genome medicine. 2018 Mar 20
PMID: 29558968
- AS03- and MF59-Adjuvanted Influenza Vaccines in Children.
Wilkins AL, Kazmin D, Napolitani G, Clutterbuck EA, Pulendran B, Siegrist CA, Pollard AJ
Frontiers in immunology. 2017
PMID: 29326687
- Cell type discovery and representation in the era of high-content single cell phenotyping.
Bakken T, Cowell L, Aevermann BD, Novotny M, Hodge R, Miller JA, Lee A, Chang I, McCorrison J, Pulendran B, Qian Y, Schork NJ, Lasken RS, Lein ES, Scheuermann RH
BMC bioinformatics. 2017 Dec 21
PMID: 29322913
- Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses.
HIPC-CHI Signatures Project Team., HIPC-I Consortium.
Science immunology. 2017 Aug 25
PMID: 28842433
- The potential of the microbiota to influence vaccine responses.
Lynn DJ, Pulendran B
Journal of leukocyte biology. 2018 Feb
PMID: 28864446
- Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types.
Mead BE, Ordovas-Montanes J, Braun AP, Levy LE, Bhargava P, Szucs MJ, Ammendolia DA, MacMullan MA, Yin X, Hughes TK, Wadsworth MH 2nd, Ahmad R, Rakoff-Nahoum S, Carr SA, Langer R, Collins JJ, Shalek AK, Karp JM
BMC biology. 2018 Jun 5
PMID: 29871632
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