Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets

[1]  M. Wegkamp,et al.  Inference in latent factor regression with clusterable features , 2022, Bernoulli.

[2]  Evan Ripley-McNeil Just Getting Started , 2022, The Journal of Individual Psychology.

[3]  Jennifer S. Wood,et al.  A yeast-expressed RBD-based SARS-CoV-2 vaccine formulated with 3M-052-alum adjuvant promotes protective efficacy in non-human primates , 2021, Science Immunology.

[4]  D. Lauffenburger,et al.  Mining for humoral correlates of HIV control and latent reservoir size , 2020, PLoS pathogens.

[5]  D. Lauffenburger,et al.  Mapping functional humoral correlates of protection against malaria challenge following RTS,S/AS01 vaccination , 2020, Science Translational Medicine.

[6]  Panos K. Chrysanthis,et al.  CausalMGM: an interactive web-based causal discovery tool , 2020, Nucleic Acids Res..

[7]  J. Marioni,et al.  MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data , 2020, Genome Biology.

[8]  Aurelien Dugourd,et al.  Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses , 2020, bioRxiv.

[9]  S. Fortune,et al.  Antibody Fc Glycosylation Discriminates Between Latent and Active Tuberculosis , 2020, The Journal of infectious diseases.

[10]  J. Leader,et al.  Feasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models , 2019, Thorax.

[11]  J. Kirkwood,et al.  PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy , 2019, Scientific Reports.

[12]  Clark Glymour,et al.  Mixed graphical models for integrative causal analysis with application to chronic lung disease diagnosis and prognosis , 2018, Bioinform..

[13]  D. Lauffenburger,et al.  Initiation of Antiretroviral Therapy Before Pregnancy Reduces the Risk of Infection-related Hospitalization in Human Immunodeficiency Virus–exposed Uninfected Infants Born in a High-income Country , 2018, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[14]  Julian Q. Zhou,et al.  Affinity Maturation Is Impaired by Natural Killer Cell Suppression of Germinal Centers , 2018, Cell reports.

[15]  D. Lauffenburger,et al.  Route of immunization defines multiple mechanisms of vaccine-mediated protection against SIV , 2018, Nature Medicine.

[16]  Dimitris V. Manatakis,et al.  piMGM: incorporating multi‐source priors in mixed graphical models for learning disease networks , 2018, Bioinform..

[17]  J. Mikes,et al.  Stereotypic Immune System Development in Newborn Children , 2018, Cell.

[18]  Vineet K Raghu,et al.  Evaluation of Causal Structure Learning Methods on Mixed Data Types , 2018, CD@KDD.

[19]  B. Pulendran,et al.  Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? From Data to Understanding through Systems Biology. , 2018, Cold Spring Harbor perspectives in biology.

[20]  Dimitris V. Manatakis,et al.  Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients , 2018, Front. Microbiol..

[21]  Hamid Alinejad-Rokny,et al.  A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis , 2018, npj Systems Biology and Applications.

[22]  Nir Hacohen,et al.  Systems Immunology: Learning the Rules of the Immune System. , 2018, Annual review of immunology.

[23]  Panos K. Chrysanthis,et al.  Comparison of strategies for scalable causal discovery of latent variable models from mixed data , 2018, International Journal of Data Science and Analytics.

[24]  D. Lauffenburger,et al.  Temporal variation in HIV-specific IgG subclass antibodies during acute infection differentiates spontaneous controllers from chronic progressors , 2017, AIDS.

[25]  Alan Wells,et al.  Biomarker identification for statin sensitivity of cancer cell lines , 2017, bioRxiv.

[26]  Mark M. Davis,et al.  Systems immunology: just getting started , 2017, Nature Immunology.

[27]  Shuzhao Li,et al.  Metabolic Phenotypes of Response to Vaccination in Humans , 2017, Cell.

[28]  M. Wegkamp,et al.  Adaptive estimation in structured factor models with applications to overlapping clustering , 2017, The Annals of Statistics.

[29]  Eva K. Lee,et al.  Systems analysis of protective immune responses to RTS,S malaria vaccination in humans , 2017, Proceedings of the National Academy of Sciences.

[30]  L. Joosten,et al.  Immunometabolic circuits in trained immunity. , 2016, Seminars in immunology.

[31]  Andrew J. Sedgewick,et al.  Learning mixed graphical models with separate sparsity parameters and stability-based model selection , 2016, BMC Bioinformatics.

[32]  Trevor Bedford,et al.  Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine. , 2015, The New England journal of medicine.

[33]  William Stafford Noble,et al.  Machine learning applications in genetics and genomics , 2015, Nature Reviews Genetics.

[34]  R. Welsh,et al.  Generation of cellular immune memory and B-cell immunity are impaired by natural killer cells , 2015, Nature Communications.

[35]  Trevor Hastie,et al.  Learning the Structure of Mixed Graphical Models , 2015, Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America.

[36]  N. Gomez‐Lopez,et al.  Immune cells in term and preterm labor , 2014, Cellular and Molecular Immunology.

[37]  Sandra Romero-Steiner,et al.  Molecular signatures of antibody responses derived from a systems biological study of 5 human vaccines , 2013, Nature Immunology.

[38]  A. Zenclussen,et al.  Cutting Edge: IL‐10‐Producing Regulatory B Cells in Early Human Pregnancy , 2013, American journal of reproductive immunology.

[39]  A. Zenclussen,et al.  Regulatory B10 Cells Restore Pregnancy Tolerance in a Mouse Model1 , 2013, Biology of reproduction.

[40]  Clifford Lam,et al.  Factor modeling for high-dimensional time series: inference for the number of factors , 2012, 1206.0613.

[41]  Eva K. Lee,et al.  Systems Biology of Seasonal Influenza Vaccination in Humans , 2011, Nature immunology.

[42]  Larry A. Wasserman,et al.  Stability Approach to Regularization Selection (StARS) for High Dimensional Graphical Models , 2010, NIPS.

[43]  Judea Pearl,et al.  The International Journal of Biostatistics C AUSAL I NFERENCE An Introduction to Causal Inference , 2011 .

[44]  M. Vidal,et al.  Literature-curated protein interaction datasets , 2009, Nature Methods.

[45]  Alison S Care,et al.  Essential Role for IL-10 in Resistance to Lipopolysaccharide-Induced Preterm Labor in Mice1 , 2006, The Journal of Immunology.

[46]  R. Tibshirani,et al.  Prediction by Supervised Principal Components , 2006 .

[47]  J. Castle,et al.  An integrative genomics approach to infer causal associations between gene expression and disease , 2005, Nature Genetics.

[48]  K. Sachs,et al.  Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data , 2005, Science.

[49]  M. Wegkamp,et al.  Prediction Under Latent Factor Regression: Adaptive PCR, Interpolating Predictors and Beyond , 2021, J. Mach. Learn. Res..

[50]  Shuzhao Li,et al.  Systems vaccinology: Probing humanity’s diverse immune systems with vaccines , 2014, Proceedings of the National Academy of Sciences.

[51]  A. Boulesteix,et al.  Partial least squares: a versatile tool for the analysis of high-dimensional genomic data , 2007, Briefings Bioinform..

[52]  R. Tibshirani,et al.  Sparse inverse covariance estimation with the graphical lasso. , 2008, Biostatistics.

[53]  L. Breiman Random Forests , 2001, Machine Learning.

[54]  R. Tibshirani Regression Shrinkage and Selection via the Lasso , 1996 .