Human Immunology Project Consortium

Recent Publications

• Functional interpretation of single cell similarity maps.
  DeTomaso D, Jones MG, Subramaniam M, Ashuach T, Ye CJ, Yosef N
  Nature communications. 2019 Sep 26
  PMID: 31558714
• 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
• 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
• 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
• 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
• The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system.
  Tomic A, Tomic I, Dekker CL, Maecker HT, Davis MM
  Scientific data. 2019 Oct 21
  PMID: 31636302
• Immunosenescence and human vaccine immune responses.
  Crooke SN, Ovsyannikova IG, Poland GA, Kennedy RB
  Immunity & ageing : I & A. 2019
  PMID: 31528180
• 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
• Immunosenescence: A systems-level overview of immune cell biology and strategies for improving vaccine responses.
  Crooke SN, Ovsyannikova IG, Poland GA, Kennedy RB
  Experimental gerontology. 2019 Sep
  PMID: 31201918
• 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
• Germline-Encoded Affinity for Cognate Antigen Enables Vaccine Amplification of a Human Broadly Neutralizing Response against Influenza Virus.
  Sangesland M, Ronsard L, Kazer SW, Bals J, Boyoglu-Barnum S, Yousif AS, Barnes R, Feldman J, Quirindongo-Crespo M, McTamney PM, Rohrer D, Lonberg N, Chackerian B, Graham BS, Kanekiyo M, Shalek AK, Lingwood D
  Immunity. 2019 Oct 15
  PMID: 31563464
• Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration.
  Pepe-Mooney BJ, Dill MT, Alemany A, Ordovas-Montanes J, Matsushita Y, Rao A, Sen A, Miyazaki M, Anakk S, Dawson PA, Ono N, Shalek AK, van Oudenaarden A, Camargo FD
  Cell stem cell. 2019 Jul 3
  PMID: 31080134
• SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses.
  Tomic A, Tomic I, Rosenberg-Hasson Y, Dekker CL, Maecker HT, Davis MM
  Journal of immunology (Baltimore, Md. : 1950). 2019 Aug 1
  PMID: 31201239
• 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
• Exploring single-cell data with deep multitasking neural networks.
  Amodio M, van Dijk D, Srinivasan K, Chen WS, Mohsen H, Moon KR, Campbell A, Zhao Y, Wang X, Venkataswamy M, Desai A, Ravi V, Kumar P, Montgomery R, Wolf G, Krishnaswamy S
  Nature methods. 2019 Oct 7
  PMID: 31591579
• 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
• 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
• 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
• Transcriptomic analysis of human IL-7 receptor alpha ^low and ^high effector memory CD8⁺ 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