Recent Publications
- A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data.
Yu T
PLoS computational biology. 2018 Aug
PMID: 30080856
- Cell-centred meta-analysis reveals baseline predictors of anti-TNF? non-response in biopsy and blood of patients with IBD.
Gaujoux R, Starosvetsky E, Maimon N, Vallania F, Bar-Yoseph H, Pressman S, Weisshof R, Goren I, Rabinowitz K, Waterman M, Yanai H, Dotan I, Sabo E, Chowers Y, Khatri P, Shen-Orr SS, Israeli IBD research Network (IIRN).
Gut. 2019 Apr
PMID: 29618496
- Deep generative modeling for single-cell transcriptomics.
Lopez R, Regier J, Cole MB, Jordan MI, Yosef N
Nature methods. 2018 Dec
PMID: 30504886
- 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
- Whole blood transcriptome changes following controlled human malaria infection in malaria pre-exposed volunteers correlate with parasite prepatent period.
Rothen J, Murie C, Carnes J, Anupama A, Abdulla S, Chemba M, Mpina M, Tanner M, Lee Sim BK, Hoffman SL, Gottardo R, Daubenberger C, Stuart K
PloS one. 2018
PMID: 29920562
- Influenza vaccine failure: failure to protect or failure to understand?
Poland GA
Expert review of vaccines. 2018 Jun
PMID: 29883218
- Linking single-cell measurements of mass, growth rate, and gene expression.
Kimmerling RJ, Prakadan SM, Gupta AJ, Calistri NL, Stevens MM, Olcum S, Cermak N, Drake RS, Pelton K, De Smet F, Ligon KL, Shalek AK, Manalis SR
Genome biology. 2018 Nov 27
PMID: 30482222
- KLRD1-expressing natural killer cells predict influenza susceptibility.
Bongen E, Vallania F, Utz PJ, Khatri P
Genome medicine. 2018 Jun 14
PMID: 29898768
- Nonlinear variable selection with continuous outcome: a fully nonparametric incremental forward stagewise approach.
Yu T
Statistical analysis and data mining. 2018 Aug
PMID: 30595785
- Detection and Quantification of Influenza A/H1N1 Virus-Specific Memory B Cells in Human PBMCs Using ELISpot Assay.
Haralambieva IH, Ovsyannikova IG, Kennedy RB, Poland GA
Methods in molecular biology (Clifton, N.J.). 2018
PMID: 29956187
- Breadth and Functionality of Varicella-Zoster Virus Glycoprotein-Specific Antibodies Identified after Zostavax Vaccination in Humans.
Sullivan NL, Reuter-Monslow MA, Sei J, Durr E, Davis CW, Chang C, McCausland M, Wieland A, Krah D, Rouphael N, Mehta AK, Mulligan MJ, Pulendran B, Ahmed R, Vora KA
Journal of virology. 2018 Jul 15
PMID: 29743372
- 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
- B Cell Competition for Restricted T Cell Help Suppresses Rare-Epitope Responses.
Woodruff MC, Kim EH, Luo W, Pulendran B
Cell reports. 2018 Oct 9
PMID: 30304673
- Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer.
Hamza B, Ng SR, Prakadan SM, Delgado FF, Chin CR, King EM, Yang LF, Davidson SM, DeGouveia KL, Cermak N, Navia AW, Winter PS, Drake RS, Tammela T, Li CM, Papagiannakopoulos T, Gupta AJ, Shaw Bagnall J, Knudsen SM, Vander Heiden MG, Wasserman SC, Jacks T, Shalek AK, Manalis SR
Proceedings of the National Academy of Sciences of the United States of America. 2019 Feb 5
PMID: 30674677
- 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
- Allergic inflammatory memory in human respiratory epithelial progenitor cells.
Ordovas-Montanes J, Dwyer DF, Nyquist SK, Buchheit KM, Vukovic M, Deb C, Wadsworth MH 2nd, Hughes TK, Kazer SW, Yoshimoto E, Cahill KN, Bhattacharyya N, Katz HR, Berger B, Laidlaw TM, Boyce JA, Barrett NA, Shalek AK
Nature. 2018 Aug
PMID: 30135581
- 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
- OX40L/OX40 axis impairs follicular and natural Treg function in human SLE.
Jacquemin C, Augusto JF, Scherlinger M, Gensous N, Forcade E, Douchet I, Levionnois E, Richez C, Lazaro E, Duffau P, Truchetet ME, Seneschal J, Couzi L, Pellegrin JL, Viallard JF, Schaeverbeke T, Pascual V, Contin-Bordes C, Blanco P
JCI insight. 2018 Dec 20
PMID: 30568041
- 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
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