Recent Publications
- Nonlinear variable selection with continuous outcome: a fully nonparametric incremental forward stagewise approach.
Yu T
Statistical analysis and data mining. 2018 Aug
PMID: 30595785
- Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans.
Hagan T, Cortese M, Rouphael N, Boudreau C, Linde C, Maddur MS, Das J, Wang H, Guthmiller J, Zheng NY, Huang M, Uphadhyay AA, Gardinassi L, Petitdemange C, McCullough MP, Johnson SJ, Gill K, Cervasi B, Zou J, Bretin A, Hahn M, Gewirtz AT, Bosinger SE, Wilson PC, Li S, Alter G, Khurana S, Golding H, Pulendran B
Cell. 2019 Sep 5
PMID: 31491384
- Simulating multiple faceted variability in single cell RNA sequencing.
Zhang X, Xu C, Yosef N
Nature communications. 2019 Jun 13
PMID: 31197158
- 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
- Elevated Activation of Neutrophil Toll-Like Receptors in Patients with Acute Severe Leptospirosis: An Observational Study.
Lindow JC, Tsay AJ, Montgomery RR, Reis EAG, Wunder EA, Araújo G, Nery NRR, Mohanty S, Shaw AC, Lee PJ, Reis MG, Ko AI
The American journal of tropical medicine and hygiene. 2019 Sep
PMID: 31333152
- 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 Jul
PMID: 31040105
- Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells.
Reitman ZJ, Paolella BR, Bergthold G, Pelton K, Becker S, Jones R, Sinai CE, Malkin H, Huang Y, Grimmet L, Herbert ZT, Sun Y, Weatherbee JL, Alberta JA, Daley JF, Rozenblatt-Rosen O, Condurat AL, Qian K, Khadka P, Segal RA, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles CD, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R
Nature communications. 2019 Aug 19
PMID: 31427603
- Transcriptomic analysis of human IL-7 receptor alpha <sup>low</sup> and <sup>high</sup> effector memory CD8<sup>+</sup> T cells reveals an age-associated signature linked to influenza vaccine response in older adults.
Park HJ, Shin MS, Kim M, Bilsborrow JB, Mohanty S, Montgomery RR, Shaw AC, You S, Kang I
Aging cell. 2019 Aug
PMID: 31044512
- Shaping of infant B cell receptor repertoires by environmental factors and infectious disease.
Nielsen SCA, Roskin KM, Jackson KJL, Joshi SA, Nejad P, Lee JY, Wagar LE, Pham TD, Hoh RA, Nguyen KD, Tsunemoto HY, Patel SB, Tibshirani R, Ley C, Davis MM, Parsonnet J, Boyd SD
Science translational medicine. 2019 Feb 27
PMID: 30814336
- HIPK2 is necessary for type I interferon-mediated antiviral immunity.
Cao L, Yang G, Gao S, Jing C, Montgomery RR, Yin Y, Wang P, Fikrig E, You F
Science signaling. 2019 Mar 19
PMID: 30890658
- Dissecting alterations in human CD8+ T cells with aging by high-dimensional single cell mass cytometry.
Shin MS, Yim K, Moon K, Park HJ, Mohanty S, Kim JW, Montgomery RR, Shaw AC, Krishnaswamy S, Kang I
Clinical immunology (Orlando, Fla.). 2019 Mar
PMID: 30659916
- 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
- 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 Jun
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
- Time varying causal network reconstruction of a mouse cell cycle.
Masnadi-Shirazi M, Maurya MR, Pao G, Ke E, Verma IM, Subramaniam S
BMC bioinformatics. 2019 May 29
PMID: 31142274
- 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
- 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
- An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data.
Mah CK, Wenzel AT, Juarez EF, Tabor T, Reich MM, Mesirov JP
F1000Research. 2018
PMID: 31316748
- Topological and functional comparison of community detection algorithms in biological networks.
Rahiminejad S, Maurya MR, Subramaniam S
BMC bioinformatics. 2019 Apr 27
PMID: 31029085
- Skeletal muscle: A review of molecular structure and function, in health and disease.
Mukund K, Subramaniam S
Wiley interdisciplinary reviews. Systems biology and medicine. 2019 Aug 13
PMID: 31407867
- A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring.
Alpert A, Pickman Y, Leipold M, Rosenberg-Hasson Y, Ji X, Gaujoux R, Rabani H, Starosvetsky E, Kveler K, Schaffert S, Furman D, Caspi O, Rosenschein U, Khatri P, Dekker CL, Maecker HT, Davis MM, Shen-Orr SS
Nature medicine. 2019 Mar
PMID: 30842675
- 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
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