Publications

Total: 56 published papers

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2024 2023 2022 2021 2020 2019 2018 2016 2015 2014 2013 2012

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Uncovering cell-type-specific immunomodulatory variants and molecular phenotypes in COVID-19 using structurally resolved protein networks
Interpretable machine learning uncovers epithelial transcriptional rewiring and a role for Gelsolin in COPD
Spatial microniches of IL-2 combine with IL-10 to drive lung migratory TH2 cells in response to inhaled allergen
Deep humoral profiling coupled to interpretable machine learning unveils diagnostic markers and pathophysiology of schistosomiasis
Tim-3 Is Required for Regulatory T Cell–Mediated Promotion of T Cell Exhaustion and Viral Persistence during Chronic Lymphocytic Choriomeningitis Virus Infection
High-dimensional profiling of immune responses to kidney transplant reveals heterogeneous T helper 1 and B cell effectors associated with rejection
Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics
Aberrant mitochondrial DNA synthesis in macrophages exacerbates inflammation and atherosclerosis
The RNA binding protein Arid5a drives IL-17-dependent autoantibody-induced glomerulonephritis
Temporal dynamics and genomic programming of plasma cell fates
Transcriptomic and Proteomic Characterization of the Immune Response to Elective Spinal Reconstructive Surgery -Impact of Aging and Comparison with Traumatic Injury Response
Regulatory T Cell Insufficiency in Autoimmune Diabetes Is Driven by Selective Loss of Neuropilin-1 on Intraislet Regulatory T Cells
Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data
SLIDE- Significant Latent factor Interaction Discovery and Exploration across biological domains
PRMT blockade induces defective DNA replication stress response and synergizes with PARP inhibition
SARS-CoV-2 mRNA vaccines induce greater complement activation and decreased viremia and Nef antibodies in men with HIV-1
From bench to bedside via bytes- multi-omic immunoprofiling and integration using machine learning and network approaches
The gut protist Tritrichomonas arnold restrains virus-mediated loss of oral tolerance by modulating dietary antigen-presenting dendritic cells
Stability and heterogeneity in the antimicrobiota reactivity of human milk-derived immunoglobulin A
High dimensional proteomics identifies organ injury patterns associated with outcomes in human trauma
Cell‐type‐specific biomarkers of systemic sclerosis disease severity capture cell‐intrinsic and cell‐extrinsic circuits
Antibodies against the Ebola virus soluble glycoprotein are associated with long-term vaccine-mediated protection of non-human primates
Landscape of microRNA regulatory network architecture and functional rerouting in cancer
Determining asthma endotypes and outcomes- Complementing existing clinical practice with modern machine learning
Lipidomic signatures align with inflammatory patterns and outcomes in critical illness
High Dimensional Multiomics Reveals Unique Characteristics of Early Plasma Administration in Polytrauma Patients With TBI
Multi-Omic Admission-Based Prognostic Biomarkers Identified by Machine Learning Algorithms Predict Patient Recovery and 30-Day Survival in Trauma Patients
A Supervised Take on Dimensionality Reduction via Hybrid Subset Selection
Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3
Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19
Essential Regression- A generalizable framework for inferring causal latent factors from multi-omic datasets
A network-based approach to identify expression modules underlying rejection in pediatric liver transplantation
Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity
Functional reprogramming of monocytes in acute and convalescent severe COVID-19 patients
Upper and lower respiratory tract correlates of protection against respiratory syncytial virus following vaccination of nonhuman primates
People critically ill with COVID-19 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 lung viral burden
Delayed fractional dosing with RTS, S/AS01 improves humoral immunity to malaria via a balance of polyfunctional NANP6-and Pf16-specific antibodies
Mechanisms of Impaired Lung Development and Ciliation in Mannosidase-1-Alpha-2 Mutants
Extracellular Matrix Injury of Kidney Allografts in Antibody-Mediated Rejection- A Proteomics Study
Mining for humoral correlates of HIV control and latent reservoir size
Glucosylation by the Legionella effector SetA promotes the nuclear localization of the transcription factor TFEB
Mapping functional humoral correlates of protection against malaria challenge following RTS, S/AS01 vaccination
Co-immunization of DNA and Protein in the Same Anatomical Sites Induces Superior Protective Immune Responses against SHIV Challenge
Latency reversal agents modulate HIV antigen processing and presentation to CD8 T cells
Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis
Antibody Fc-glycosylation discriminates latent and active tuberculosis
Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations
Antibiotics-driven gut microbiome perturbation alters immunity to vaccine in humans
Effect of dietary fat and sucrose consumption on cardiac fibrosis in mice and rhesus monkeys
Fc glycan-mediated regulation of placental antibody transfer
Genetic polymorphisms in the open reading frame of the CCR5 gene from HIV-1 seronegative and seropositive individuals from national capital regions of India
Latent model-based clustering for biological discovery
Initiation of anti-retroviral therapy before pregnancy reduces the risk of infection related hospitalization in HIV-exposed uninfected infants
Analysis of Complement mediated lysis of SIV and SIV-infected cells reveals sex differences in vaccine-induced immune responses and protection from infection in Rhesus macaques
Route of immunization defines multiple mechanisms of vaccine-mediated protection against SIV
A role for Fc function in therapeutic monoclonal antibody-mediated protection against Ebola virus
Control of heterologous SIVsmE660 infection by DNA and protein co-immunization regimens combined with different Toll-like receptor-4 (TLR-4) based adjuvants in macaques
A multi-landing pad DNA integration platform for mammalian cell engineering
The transcription factors Runx3, T-bet and ThPOK co-regulate acquisition of cytotoxic function by human Th1 lymphocytes
Temporal variation in HIV-specific IgG subclass antibodies during acute infection differentiates spontaneous 4 controllers from chronic progressors
Mutation3D-cancer gene prediction through atomic clustering of coding variants in the structural proteome
A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human
Studying autism in context
Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replication
ENCAPP-elastic-net-based prognosis prediction and biomarker discovery for human cancers
A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations
Predicting cancer prognosis using functional genomics datasets
Exploring mechanisms of human disease through structurally-resolved protein interactome networks
Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks
Dissecting disease inheritance modes in a 3D protein network challenges the guilt-by-association principle
INstruct - a database of high-quality 3D structurally resolved protein interactome networks
Integrative annotation of variants from 1,092 humans- application to cancer genomics
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways
HINT:High quality interactomes and their applications in understanding human disease
Genome-scale analysis of interaction dynamics reveals organization of biological networks
Three-dimensional reconstruction of protein networks provides insight into human genetic disease