Our Deep Focus Playlist
Publications (85)
Gasdermin D drives the systemic storm and mortality after trauma with hemorrhage to a greater degree in biological females than males
05/28/2025 - Science Translational Medicine
Sun X, Abdelhamid SS, Secunda Z, Voinchet R, [...], Neal MD, Kar UK, Sperry JL, Billiar TR
Unique and shared transcriptomic signatures underlying localized scleroderma pathogenesis identified using interpretable machine learning
04/08/2025 - JCI Insight
Rosen AB*, Sanyal A*, Werner THG, Berkowitz JS, [...], Lafyatis R, Jacobe H, Das J^, Torok KS^
Machine learning approaches enable the discovery of therapeutics across domains
04/03/2025 - Molecular Therapy
Chhibbar P^, Das J^
Immuno-oncology recapitulates ontogeny- Modern cell and gene therapy for cancer
03/28/2025 - Molecular Therapy
Carleton N, Rosen AB, Das J, Lotze MT
High-dimensional analysis of injured patients reveals distinct circulating proteomic profiles in plasma vs. whole blood resuscitation
03/18/2025 - Cell Reports Medicine
Moheimani H, Sun X, Ozel M, Darby JL, [...], Barrett CD, Das J, Sperry JL, Billiar TR
Opportunities in AI/ML to endotype asthma and other eosinophilic diseases
02/14/2025 - Journal of Allergy and Clinical Immunology
Ray A^, Das J^, Khoury P^
Dysfunctional KLRB1+CD8+ T-cell responses are generated in chronically inflamed systemic sclerosis skin
02/01/2025 - Annals of the Rheumatic Diseases
Gaydosik AM, Tabib T, Das J, Larregina A, Lafyatis R, Fuschiotti P
The survival of B cells is compromised in kidney disease
12/30/2024 - Nature Communications
Peroumal D, Jawale CV, Choi W, Rahimi H, [...], Nolin TD, Das J, Alcorn JF, Biswas PS
Agonism of the glutamate receptor GluK2 suppresses dermal mast cell activation and cutaneous inflammation
12/11/2024 - Science Translational Medicine
Zhang YR, Keshari S, Kurihara K, Liu J, [...], Falo LD Jr, Das J, Sumpter TL, Kaplan DH
Uncovering cell-type-specific immunomodulatory variants and molecular phenotypes in COVID-19 using structurally resolved protein networks
11/24/2024 - Cell Reports
Chhibbar P*, Roy P*, Harioudh M*, McGrail D, [...], Yi SS, Sahni N, Sarkar S, Das J^
Interpretable machine learning uncovers epithelial transcriptional rewiring and a role for Gelsolin in COPD
11/08/2024 - The Journal of Clinical Investigation Insight
Sui J*, Xiao H*, Mbaekwe U, Ting NC, [...], Zhang Y, Sciurba FC, Das J^, Kliment C^
Spatial microniches of IL-2 combine with IL-10 to drive lung migratory TH2 cells in response to inhaled allergen
10/14/2024 - Nature Immunology
He K, Xiao H, MacDonald WA, Mehta I, [...], Weaver CT, Lambrecht BN, Das J, Poholek AC
Deep humoral profiling coupled to interpretable machine learning unveils diagnostic markers and pathophysiology of schistosomiasis
09/11/2024 - Science Translational Medicine
Saha A*, Chakraborty T*, Rahimikollu J, Xiao H, [...], A OFraga L, Fairley JK^, Das J^, Sarkar A^
Tim-3 Is Required for Regulatory T Cell,??Mediated Promotion of T Cell Exhaustion and Viral Persistence during Chronic Lymphocytic Choriomeningitis Virus Infection
08/30/2024 - Journal of Immunology
Nieves-Rosado H, Banerjee H, Gocher-Demske A, Manandhar P, [...], Das J, Vignali D, Delgoffe G, Kane L
Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics
08/12/2024 - PLoS Computational Biology
Chavez R, Fili M, Han C, Rahman S, [...], Darbro B, Das J, Brown G, Haim H
High-dimensional profiling of immune responses to kidney transplant reveals heterogeneous T helper 1 and B cell effectors associated with rejection
08/12/2024 - American Journal of Transplantation
Louis K, Tabib T, Macedo C, Wang J, [...], Das J, Singh H, Lefaucheur C, Metes D
Aberrant mitochondrial DNA synthesis in macrophages exacerbates inflammation and atherosclerosis
08/11/2024 - Nature Communications
Natarajan N, Florentin J, Johny E, Xiao H, [...], Tavakoli S, Shiva S, Das J, Dutta P
The RNA binding protein Arid5a drives IL-17-dependent autoantibody-induced glomerulonephritis
07/12/2024 - Journal of Experimental Medicine
Li Y, Vyas S, Mehta I, Asada N, [...], Biswas P, Savan R, Das J, Gaffen S
Temporal dynamics and genomic programming of plasma cell fates
06/19/2024 - Nature Immunology
Kumar G, Zhou M, Thakkar K, Rothrauff A, [...], Borghesi L, Salomonis N, Xu H, Singh H
Transcriptomic and Proteomic Characterization of the Immune Response to Elective Spinal Reconstructive Surgery -Impact of Aging and Comparison with Traumatic Injury Response
05/12/2024 - Journal of the American College of Surgeons
Bonaroti J, Ozel M, Chen T, Darby J, [...], Kar U Zuckerbraun B, Das J, Okonkwo D, Billiar T
Regulatory T Cell Insufficiency in Autoimmune Diabetes Is Driven by Selective Loss of Neuropilin-1 on Intraislet Regulatory T Cells
03/25/2024 - Journal of Immunology
Grebinoski S, Pieklo G, Zhang Q, Visperas A, [...], Herrada A, Das J, Workman C, Vignali D
Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data
03/25/2024 - Nature Computational Science
Osorio D, Capasso A, Eckhardt S, Giri U, [...], Das J, Sahni N, Yi S, Kuijjer M
SLIDE- Significant Latent factor Interaction Discovery and Exploration across biological domains
02/19/2024 - Nature Methods
Rahimikollu J*, Xiao H*, Rosengart A, Rosen A, [...], Poholek A^, Joglekar A^, Lafyatis R^, Das J^
PRMT blockade induces defective DNA replication stress response and synergizes with PARP inhibition
12/19/2023 - Cell Reports Medicine
Li H, Dobrolecki L, Sallas C, Zhang X, [...], Yi S, Bedford M, McGrail D, Sahni N
SARS-CoV-2 mRNA vaccines induce greater complement activation and decreased viremia and Nef antibodies in men with HIV-1
11/30/2023 - The Journal of Infectious Diseases
Tuttle D, Castanha P, Nasser A, Wilkins M, [...], Mailliard R, Sluis-Cremer N, Rinaldo C, Marques E
From bench to bedside via bytes- multi-omic immunoprofiling and integration using machine learning and network approaches
11/09/2023 - Human Vaccines & Immunotherapeutics
Xiao H*, Rosen A*, Chhibbar P*, Moise L, Das J^
The gut protist Tritrichomonas arnold restrains virus-mediated loss of oral tolerance by modulating dietary antigen-presenting dendritic cells
08/08/2023 - Immunity
Sanchez L, Siller M, Zeng Y, Brigleb P, [...], Das J, Dermody T, Verdu E, Hinterleitner R
Stability and heterogeneity in the antimicrobiota reactivity of human milk-derived immunoglobulin A
07/18/2023 - Journal of Experimental Medicine
Johnson-Hence C, Gopalakrishna K, Bodkin D, Coffey K, [...], Sosa Y, Tometich J, Das J, Hand T
High dimensional proteomics identifies organ injury patterns associated with outcomes in human trauma
06/04/2023 - Journal of Trauma and Acute Care Surgery
Li SR, Moheimani H, Herzig B, Kail M, [...], Das J, Kar U, Sperry J, Billiar TR
Cell Type-Specific Biomarkers of Systemic Sclerosis Disease Severity Capture Cell-Intrinsic and Cell-Extrinsic Circuits
04/25/2023 - Arthritis and Rheumatology
Berkowitz J, Tabib T, Xiao H, Sadej GM, [...], Khanna D, Fuschiotti P, Lafyatis R^, Das J^
Antibodies against the Ebola virus soluble glycoprotein are associated with long-term vaccine-mediated protection of non-human primates
04/25/2023 - Cell Reports Medicine
Gunn B, McNamara R, Wood L, Taylor S, [...], Nilsson A, Shurtleff A, Dubey S, Eichberg M
Landscape of microRNA regulatory network architecture and functional rerouting in cancer
01/04/2023 - Cancer Research
Hua X, Li Y, Pentaparthi SR, McGrail DJ, [...], Wu E, Huang JH, Sahni N, Yi SS
Lipidomic signatures align with inflammatory patterns and outcomes in critical illness
11/10/2022 - Nature Communications
Wu J, Cyr A, Danielle G, Lovelace T, [...], Stensballe J, Namas R, Vodovotz Y, Sperry J
Determining asthma endotypes and outcomes- Complementing existing clinical practice with modern machine learning
11/10/2022 - Cell Reports Medicine
Ray A^, Das J^, Wenzel S^
High Dimensional Multiomics Reveals Unique Characteristics of Early Plasma Administration in Polytrauma Patients With TBI
10/14/2022 - Annals of Surgery
Wu J, Moheimani H, Li S, Kar U, [...], Neal M, Das J^, Sperry J^, Billiar T^
Multi-Omic Admission-Based Prognostic Biomarkers Identified by Machine Learning Algorithms Predict Patient Recovery and 30-Day Survival in Trauma Patients
08/23/2022 - Metabolites
Abdelhamid S, Scioscia J, Vodovotz Y, Wu J, [...], Neal MD, Sperry J, Das J^, Billiar TR^
A Supervised Take on Dimensionality Reduction via Hybrid Subset Selection
08/12/2022 - Patterns
Rahimikollu J*, Das J^
Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3
07/26/2022 - Nature Immunology
Grebinoski S, Zhang Q, Cillo AR, Manne S, [...], Wherry EJ, Das J, Workman CJ, Vignali DAA^
Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19
06/28/2022 - Cell Reports
Peddireddy SP*, Rahman S*, Cillo AR, Vijay GM, [...], Morris A, Singh H^, Sarkar A^, Das J^
Essential Regression- A generalizable framework for inferring causal latent factors from multi-omic datasets
05/13/2022 - Patterns
Bing X*, Lovelace T*, Bunea F, Wegkamp M, [...], Kasturi S, Singh H^, Benos P^, Das J^
A network-based approach to identify expression modules underlying rejection in pediatric liver transplantation
04/19/2022 - Cell Reports Medicine
Ningappa M*, Rahman S*, Higgs B.W, Ashokkumar C, Sahni N, Sindhi R^, Das J^
Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity
04/13/2022 - Cell Host & Microbe
Li D, Jawale C, Zhou C, Lin L, [...], Gaffen S, Biswas P, Dubey S, Eichberg M
Functional reprogramming of monocytes in acute and convalescent severe COVID-19 patients
04/05/2022 - JCI Insight
Brauns E, Azouz A, Grimaldi D, Xiao H, [...], Dauby N, Das J, Marchant A, Goriely S
Upper and lower respiratory tract correlates of protection against respiratory syncytial virus following vaccination of nonhuman primates
01/12/2022 - Cell Host Microbe
Zohar T, Hsiao J, Mehta N, Das J, [...], Espeseth A, Lauffenburger D, Bett A, Alter G
People critically ill with COVID-19 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 lung viral burden
12/21/2021 - Cell Reports Medicine
Cillo A, Somasundaram A, Shan F, Cardello C, [...], Singh H, Morris A, Bruno T, Vignali D
Delayed fractional dosing with RTS, S/AS01 improves humoral immunity to malaria via a balance of polyfunctional NANP6-and Pf16-specific antibodies
11/12/2021 - Med
Das J*, Fallon J*, Yu T*, Michell A, [...], Lauffenburger D A, Jongert E, Wille-Reece U, Alter G
Mechanisms of Impaired Lung Development and Ciliation in Mannosidase-1-Alpha-2 Mutants
07/13/2021 - Frontiers in Physiology
Ningappa N, Adenuga N, Ngo K, Mohamed N, [...], Gittes G, Lo C, Subramaniam S, Sindhi R
Extracellular Matrix Injury of Kidney Allografts in Antibody-Mediated Rejection- A Proteomics Study
11/08/2020 - The Journal Of American Society of Nephrology
Clotet-Freixas S, McEvoy C, Batruch I, Pastrello C, [...], Jurisica I, Chruscinski A, John R, Konvalinka A
Mining for humoral correlates of HIV control and latent reservoir size
10/13/2020 - PLOS Pathogens
Das J*, Devadhasan A, Linde C, Broge T, [...], Julg B, Deeks S, Lauffenburger D, Alter G
Glucosylation by the Legionella effector SetA promotes the nuclear localization of the transcription factor TFEB
07/24/2020 - iScience
Beck W, Kim D, Das J, Yu H, Marcus B, Smolka M, Mao Y
Mapping functional humoral correlates of protection against malaria challenge following RTS, S/AS01 vaccination
07/22/2020 - Science Translational Medicine
Suscovich T*, Fallon J*, Das J*, Demas A*, [...], Bhatia S, Jongert E, Wilke-Reece U, Alter G
Co-immunization of DNA and Protein in the Same Anatomical Sites Induces Superior Protective Immune Responses against SHIV Challenge
05/12/2020 - Cell Reports
Felber B, Lu Z, Hu Z, Valentin A, [...], Ferrari G, Ackerman M, Haynes B, Pavlakis G
Latency reversal agents modulate HIV antigen processing and presentation to CD8 T cells
03/20/2020 - PLoS Pathogens
Boucau J, Das J, Joshi N, Le Gall S
Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis
03/04/2020 - Journal of Hepatology
Weichselbaum L, Azouz A, Smolen K, Das J, [...], Trepo E, Libert F, Gustot T, Goriely S
Antibody Fc-glycosylation discriminates latent and active tuberculosis
02/20/2020 - The Journal of Infectious Diseases
Lu L*, Das J*, Grace P, Fortune S, Restrepo B, Alter G
Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations
09/12/2019 - Nature Communications
Fragoza R*, Das J*, Wierbowski S, Liang J, [...], Keinan A, Schimenti J, Clark A, Yu H
Antibiotics-driven gut microbiome perturbation alters immunity to vaccine in humans
09/05/2019 - Cell
Hagan T, Cortese M, Rouphael N, Boudreau C, [...], Alter G, Khurana S, Golding H, Pulendran B
Effect of dietary fat and sucrose consumption on cardiac fibrosis in mice and rhesus monkeys
08/15/2019 - JCI Insight
Natarajan N, Vujic A, Das J, Wang A, [...], Vaughan K, Colman R, Mattison J, Lee R
Fc glycan-mediated regulation of placental antibody transfer
07/27/2019 - Cell
Jennewein M, Goldfarb I, Dolatshahi S, Cosgrove C, [...], Lauffenburger D, Kim A, Riley L, Alter G
Genetic polymorphisms in the open reading frame of the CCR5 gene from HIV-1 seronegative and seropositive individuals from national capital regions of India
05/20/2019 - Scientific Reports
Ronsard L, Sood V, Yousif A, Ramesh J, [...], Sridharan S, Dorschel A, Ramachandran V, Banerjea A
Latent model-based clustering for biological discovery
04/26/2019 - iScience
Bin X, Royer M, Bunea F, Wegkamp M, Das J^
Initiation of anti-retroviral therapy before pregnancy reduces the risk of infection related hospitalization in HIV-exposed uninfected infants
09/12/2018 - Clinical Infectious Diseases
Goetghebuer T*, Smolen K*, Adler C*, Das J*, [...], Lauffenburger DA, Alter G, Levy J, Marchant A
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
09/12/2018 - Journal of Virology
Miller-Novak L, Das J, Musich T, Demberg T, [...], Tuero I, Ackerman M, Alter G, Robert-Guroff M
Route of immunization defines multiple mechanisms of vaccine-mediated protection against SIV
09/03/2018 - Nature Medicine
Ackerman M, Das J, Pittala S, Broge T, [...], Lauffenburger D, Bailey-Kellogg C, Roederer M, Alter G
A role for Fc function in therapeutic monoclonal antibody-mediated protection against Ebola virus
08/08/2018 - Cell Host Microbe
Gunn B, Yu W, Karim M, Brannan J, [...], Andersen K, Dye J, Saphire E, Alter G
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
07/17/2018 - Journal of Virology
Singh S, Ramirez-Salazar E, Doueiri R, Valentin A, [...], Venzon D, Hirsch V, Pavlakis G, Felber B
A multi-landing pad DNA integration platform for mammalian cell engineering
04/02/2018 - Nucleic Acids Research
Gaidukov L, Wroblewska L, Teague B, Nelson T, [...], Summers N, Lu T, Zhang L, Weiss R
The transcription factors Runx3, T-bet and ThPOK co-regulate acquisition of cytotoxic function by human Th1 lymphocytes
02/28/2018 - eLife
Serroukh Y, Gu-Trantien C, Hooshiar Kashani B, Defrance M, [...], Dalod M, Fuks F, Goriely S, Marchant A
Temporal variation in HIV-specific IgG subclass antibodies during acute infection differentiates spontaneous 4 controllers from chronic progressors
02/20/2018 - AIDS
Sadanand S*, Das J*, Chung A*, Schoen M, [...], Little S, Lauffenburger D, Richman D, Alter G
Mutation3D-cancer gene prediction through atomic clustering of coding variants in the structural proteome
02/03/2016 - Human Mutation
Meyer M, Lapcevic R, Romero A, Yoon M, [...], Stenson P, Cooper D, Paccanaro A, Yu H
A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human
01/14/2016 - Cell
Vo T*, Das J*, Meyer M*, Cordero N, [...], Roth F, Pleiss J, Xia Y, Yu H
Studying autism in context
11/25/2015 - Cell Systems
Das J*, Meyer M*, Yu H
Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replication
11/25/2015 - Molecular Cell
de Oliviera F, Kim D, Cussiol J, Das J, [...], Doerfler L, Schmidt K, Yu H, Smolka M
ENCAPP-elastic-net-based prognosis prediction and biomarker discovery for human cancers
03/16/2015 - BMC Genomics
Das J*, Gayvert K*, Bunea F, Wegkamp M, Yu H
A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations
12/11/2014 - PLoS Genetics
Wei X*, Das J*, Fragoza R*, Liang J*, [...], Cooper D, Lipkin S, Smolka M, Yu H
Predicting cancer prognosis using functional genomics datasets
11/02/2014 - Cancer Informatics
Das J*, Gayvert K*, Yu H
Exploring mechanisms of human disease through structurally-resolved protein interactome networks
03/05/2014 - Molecular BioSystems
Das J*, Fragoza R*, Lee H, Cordero N, [...], Meyer M, Vo T, Wang X, Yu H
Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks
01/01/2014 - Human Mutation
Das J, Lee H, Sagar A, Fragoza R, [...], Mort M, Stenson P, Cooper D, Yu H
Dissecting disease inheritance modes in a 3D protein network challenges the guilt-by-association principle
07/11/2013 - American Journal of Human Genetics
Guo Y, Wei X, Das J, Grimson A, Lipkin S, Clark A, Yu H
INstruct - a database of high-quality 3D structurally resolved protein interactome networks
06/11/2013 - Bioinformatics
Meyer M*, Das J*, Wang X*, Yu H
Integrative annotation of variants from 1,092 humans- application to cancer genomics
05/21/2013 - Science
Khurana E, Fu Y, Colonna V, Mu X, [...], Yu H, Rubin M, Tyler-Smith C, Gerstein M
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways
05/21/2013 - Science Signaling
Das J*, Vo T*, Wei X, Mellor J, [...], Lipkin S, Yoshida M, Roth F, Yu H
HINT:High quality interactomes and their applications in understanding human disease
07/30/2012 - BMC Systems Biology
Das J*, Yu H
Genome-scale analysis of interaction dynamics reveals organization of biological networks
07/14/2012 - Bioinformatics
Das J*, Mohammed J*, Yu H
Three-dimensional reconstruction of protein networks provides insight into human genetic disease
01/15/2012 - Nature Biotechnology
Wang X*, Wei X*, Thijssen B*, Das J*, Lipkin S, Yu H