Recent Publications
- The role of systems biology approaches in determining molecular signatures for the development of more effective vaccines.
Pezeshki A, Ovsyannikova IG, McKinney BA, Poland GA, Kennedy RB
Expert review of vaccines. 2019 Mar
PMID: 30700167
- Deep generative modeling for single-cell transcriptomics.
Lopez R, Regier J, Cole MB, Jordan MI, Yosef N
Nature methods. 2018 Dec
PMID: 30504886
- Topological and functional comparison of community detection algorithms in biological networks.
Rahiminejad S, Maurya MR, Subramaniam S
BMC bioinformatics. 2019 Apr 27
PMID: 31029085
- 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
- Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination.
Neu KE, Guthmiller JJ, Huang M, La J, Vieira MC, Kim K, Zheng NY, Cortese M, Tepora ME, Hamel NJ, Rojas KT, Henry C, Shaw D, Dulberger CL, Pulendran B, Cobey S, Khan AA, Wilson PC
The Journal of clinical investigation. 2019 Jan 2
PMID: 30457979
- Th1/Th17 polarization persists following whole-cell pertussis vaccination despite repeated acellular boosters.
da Silva Antunes R, Babor M, Carpenter C, Khalil N, Cortese M, Mentzer AJ, Seumois G, Petro CD, Purcell LA, Vijayanand P, Crotty S, Pulendran B, Peters B, Sette A
The Journal of clinical investigation. 2018 Aug 31
PMID: 29920186
- 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
- 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
- Mechanisms of lymphoma clearance induced by high-dose alkylating agents.
Lossos C, Liu Y, Kolb KE, Christie AL, van Scoyk A, Prakadan SM, Shigemori K, Stevenson KE, Morrow S, Plana OD, Fraser C, Jones KL, Liu H, Pallasch CP, Modiste R, Nguyen QD, Craig JW, Morgan EA, Vega F, Aster JC, Sarosiek KA, Shalek AK, Hemann MT, Weinstock DM
Cancer discovery. 2019 Apr 30
PMID: 31040105
- 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
- Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing.
Aicher TP, Carroll S, Raddi G, Gierahn T, Wadsworth MH 2nd, Hughes TK, Love C, Shalek AK
Methods in molecular biology (Clifton, N.J.). 2019
PMID: 31028635
- 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
- Aedes aegypti AgBR1 antibodies modulate early Zika virus infection of mice.
Uraki R, Hastings AK, Marin-Lopez A, Sumida T, Takahashi T, Grover JR, Iwasaki A, Hafler DA, Montgomery RR, Fikrig E
Nature microbiology. 2019 Mar 11
PMID: 30858571
- Current perspectives in assessing humoral immunity after measles vaccination.
Haralambieva IH, Kennedy RB, Ovsyannikova IG, Schaid DJ, Poland GA
Expert review of vaccines. 2019 Jan
PMID: 30585753
- 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
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