Our Deep Focus Playlist

Publications (83)

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, [...], 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 ABI, Das J, Lotze MT

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, [...], 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, [...], 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*, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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 - Nature Computational Science
Grebinoski S, Pieklo G, Zhang Q, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], Dermody T, Verd? 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, [...], 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, [...], 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, [...], 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 BM, McNamara RP, Wood L, [...], 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, [...], 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, [...], 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, [...], 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 SS, Scioscia J, Vodovotz Y, [...], 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, [...], 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, [...], 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, [...], Singh H, Benos P.V, 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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*, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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*, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], Colman R, Mattison J, Lee R

Fc glycan-mediated regulation of placental antibody transfer

07/27/2019 - Cell
Jennewein M, Goldfarb I, Dolatshahi S, [...], 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.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*, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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*, [...], 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, [...], 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*, [...], 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, [...], 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*, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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, [...], 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

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