Deep humoral profiling coupled to interpretable machine learning unveils diagnostic markers and pathophysiology of schistosomiasis

Saha A*, Chakraborty T*, Rahimikollu J, Xiao H, de Oliveira LBP, Hand TW, Handali S, Secor WE, A OFraga L, Fairley JK✝, Das J✝, Sarkar A✝

Science Translational Medicine 2024

SARS-CoV-2 mRNA vaccines induce greater complement activation and decreased viremia and Nef antibodies in men with HIV-1

Tuttle D, Castanha P, Nasser A, Wilkins M, Galarza T, Alaoui-El-Azher M, Cuff D, Chhibbar P, Das J, Li Y, Barratt-Boyes S, Mailliard R, Sluis-Cremer N, Rinaldo C, Marques E

The Journal of Infectious Diseases 2023

Antibodies against the Ebola virus soluble glycoprotein are associated with long-term vaccine-mediated protection of non-human primates

Gunn BM, McNamara RP, Wood L, Taylor S, Devadhasan A, Guo W, Das J, Nilsson A, Shurtleff A, Dubey S, Eichberg M

Cell Reports Medicine 2023

Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19

Peddireddy SP*, Rahman S*, Cillo AR, Vijay GM, Somasundaram A, Workman CJ, Bain W, McVerry BJ, Methe B, Lee JS, Ray P, Ray A, Bruno TC, Vignali DAA, Kitsios GD, Morris A, Singh H✝, Sarkar A✝, Das J✝

Cell Reports 2022

Upper and lower respiratory tract correlates of protection against respiratory syncytial virus following vaccination of nonhuman primates

Zohar T, Hsiao J, Mehta N, Das J, Devadhasan A, Karpinski W, Callahan C, Citron M.P, DiStefano D, Touch S, Wen Z, Sachs J, Cejas P, Espeseth A, Lauffenburger D, Bett A, Alter G

Cell Host Microbe 2022

Delayed fractional dosing with RTS, S/AS01 improves humoral immunity to malaria via a balance of polyfunctional NANP6-and Pf16-specific antibodies

Das J*, Fallon J K*, Yu T C*, Michell A, Suscovich T J, Linde C, Natarajan H, Weiner J, Coccia M, Gregory S, Ackerman M E, Bergmann-Leitner E, Fontana L, Dutta S, Lauffenburger D A, Jongert E, Wille-Reece U, Alter G

Med 2021

Extracellular Matrix Injury of Kidney Allografts in Antibody-Mediated Rejection- A Proteomics Study

Clotet-Freixas S, McEvoy C, Batruch I, Pastrello C, Kotlyar M, Van J, Arambewela M, Boshart A, Farkona S, Niu Y, Li Y, Famure O, Bozovic A, Kulasingam V, Chen P, Kim J, Chan E, Moshkelgosha S, Rahman S, Das J, Martinu T, Juvet S, Jurisica I, Chruscinski A, John R, Konvalinka A

The Journal Of American Society of Nephrology 2020

Mining for humoral correlates of HIV control and latent reservoir size

Das J*, Devadhasan A, Linde C, Broge T, Sassic J, Mangano M, O Keefe S, Suscovich TJ, Streeck H, Irrinki A, Pohlmeyer C, Min-Oo G, Lin S, Weiner JA, Cihlar T, Ackerman ME, Julg B, Deeks S, Lauffenburger D, Alter G

PLOS Pathogens 2020

Mapping functional humoral correlates of protection against malaria challenge following RTS, S/AS01 vaccination

Suscovich T*, Fallon J*, Das J*, Demas A*, Crain J, Linde C, Michell A, Natarajan H, Arevalo C, Broge T, Linnekin T, Kulkarni V, Lu R, Luedemann C, Marquette M, March S, Weiner JA, Zavala F, Gregory S, Coccia M, Flores-Garcia Y, Ackerman ME, Bergmann-Leitner E, Lauffenburger D, Hendriks J, Sadoff J, Bhatia S, Jongert E, Wilke-Reece U, Alter G

Science Translational Medicine 2020

Co-immunization of DNA and Protein in the Same Anatomical Sites Induces Superior Protective Immune Responses against SHIV Challenge

Felber B, Lu Z, Hu Z, Valentin A, Rosati M, Remmel C, Weiner J, Carpenter M, Faircloth K, Stanfield-Oakley S, Williams W, Shen X, Tomaras G, LaBranche C, Montefiori D, Trinh H, Rao M, Alam M, Vandergrift N, O Saunders K, Wang Y, Rountree W, Das J, Alter G, Reed S, Aye P, Schiro F, Pahar B, Dufour J, Veazey R, Marx P, Venzon D, Shaw G, Ferrari G, Ackerman M, Haynes B, Pavlakis G

Cell Reports 2020

Antibody Fc-glycosylation discriminates latent and active tuberculosis

Lu L*, Das J*, Grace P, Fortune S, Restrepo B, Alter G

The Journal of Infectious Diseases 2020

Antibiotics-driven gut microbiome perturbation alters immunity to vaccine in humans

Hagan T, Cortese M, Rouphael N, Boudreau C, Linde C, Maddur M, Das J, Wang H, Guthmiller J, Zheng N, Huang M, Uphadhyay A, Gardinassi L, Petitdemange C, McCullough M, Johnson S, Gill K, Cervasi B, Zou J, Bretin A, Hahn M, Gewirtz A, Bosinger S, Wilson P, Li S, Alter G, Khurana S, Golding H, Pulendran B

Cell 2019

Fc glycan-mediated regulation of placental antibody transfer

Jennewein M, Goldfarb I, Dolatshahi S, Cosgrove C, Noelette F, Krykbaeva M, Das J, Sarkar A, Gorman M, Fischinger S, Boudreau C, Brown J, Cooperrider J, Aneja J, Suscovich T, Graham B, Lauer G, Goetghebuer T, Marchant A, Lauffenburger D, Kim A, Riley L, Alter G

Cell 2019

Initiation of anti-retroviral therapy before pregnancy reduces the risk of infection related hospitalization in HIV-exposed uninfected infants

Goetghebuer T*, Smolen K*, Adler C*, Das J*, McBride T, Smits G, Lecomte S, Haelterman E, Barlow P, Piedra PA, van der Klis F, Kollmann TR, Lauffenburger DA, Alter G, Levy J, Marchant A

Clinical Infectious Diseases 2018

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

Miller-Novak L, Das J, Musich T, Demberg T, Weiner J, Venzon D, Mohanram V, Vargas-Inchaustegui D, Tuero I, Ackerman M, Alter G, Robert-Guroff M

Journal of Virology 2018

Route of immunization defines multiple mechanisms of vaccine-mediated protection against SIV

Ackerman M*, Das J*, Pittala S*, Broge T, Linde C, Suscovich T, Brown E, Bradley T, Natarajan H, Lin S, Sassic J, OKeefe S, Mehta N, Goodman D, Sips M, Weiner J, Tomaras G, Haynes B, Lauffenburger D, Bailey-Kellogg C, Roederer M, Alter G

Nature Medicine 2018

A role for Fc function in therapeutic monoclonal antibody-mediated protection against Ebola virus

Gunn B, Yu W, Karim M, Brannan J, Herbert A, Wec A, Halfmann P, Fusco M, Schendel S, Gangavarapu K, Krause T, Qiu X, He S, Das J, Suscovich T, Lai J, Chandran K, Zeitlin L, Crowe Jr J, Lauffenburger D, Kawaoka Y, Kobinger G, Andersen K, Dye J, Saphire E, Alter G

Cell Host Microbe 2018

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

Singh S, Ramírez-Salazar E, Doueiri R, Valentin A, Rosati M, Hu X, Keele B, Shen X, Tomaras G, Ferrari G, LaBranche C, Montefiori D, Das J, Alter G, Trinh H, Hamlin C, Rao M, Dayton F, Bear J, Chowdhury B, Alicea C, Lifson J, Broderick K, Sardesai N, Sivananthan S, Fox C, Reed S, Venzon D, Hirsch V, Pavlakis G, Felber B

Journal of Virology 2018

Temporal variation in HIV-specific IgG subclass antibodies during acute infection differentiates spontaneous 4 controllers from chronic progressors

Sadanand S*, Das J*, Chung A*, Schoen M, Lane S, Suscovich T, Streeck H, Smith D, Little S, Lauffenburger D, Richman D, Alter G

AIDS 2018

Tim-3 Is Required for Regulatory T Cell–Mediated Promotion of T Cell Exhaustion and Viral Persistence during Chronic Lymphocytic Choriomeningitis Virus Infection

Nieves-Rosado H, Banerjee H, Gocher-Demske A, Manandhar P, Mehta I, Ezenwa O, Xie B, Murter B, Das J, Vignali D, Delgoffe G, Kane L

Journal of Immunology 2024

High-dimensional profiling of immune responses to kidney transplant reveals heterogeneous T helper 1 and B cell effectors associated with rejection

Louis K, Tabib T, Macedo C, Wang J, Cantalupo P,Chandran U, Gu X, Lucas M, Randhawa P, Abundis M, Das J, Singh H, Lefaucheur C, Metes D

American Journal of Transplantation 2024

Aberrant mitochondrial DNA synthesis in macrophages exacerbates inflammation and atherosclerosis

Natarajan N, Florentin J, Johny E, Xiao H, O’Neil S, Lei L, Shen J, Ohayon L, Johnson A, Rao K, Li X, Zhao Y, Zhang Y, Tavakoli S, Shiva S, Das J, Dutta P

Nature Communications 2024

The RNA binding protein Arid5a drives IL-17-dependent autoantibody-induced glomerulonephritis

Li Y, Vyas S, Mehta I, Asada N, Dey I, Taylor T, Bechara R, Amatya N, Aggor F, Coleman B, Li D, Yamamoto K, Ezenwa O, Sun Y, Sterneck E, McManus C, Panzer U, Biswas P, Savan R, Das J, Gaffen S

Journal of Experimental Medicine 2024

Temporal dynamics and genomic programming of plasma cell fates

Kumar G, Zhou M, Thakkar K, Rothrauff A, Chawla A, Chen D, Lau L, Gerges P, Chetal K, Chhibbar P, Fan J, Das J, Joglekar A, Borghesi L, Salomonis N, Xu H, Singh H

Nature Immunology 2024

Regulatory T Cell Insufficiency in Autoimmune Diabetes Is Driven by Selective Loss of Neuropilin-1 on Intraislet Regulatory T Cells

Grebinoski S, Pieklo G, Zhang Q, Visperas A, Cui J, Goulet J, Xiao H, Brunazzi E, Cardello C, Herrada A, Das J, Workman C, Vignali D

Nature Computational Science 2024

The gut protist Tritrichomonas arnold restrains virus-mediated loss of oral tolerance by modulating dietary antigen-presenting dendritic cells

Sanchez L, Siller M, Zeng Y, Brigleb P, Sangani K, Soto A, Engl C, Laughlin C, Mohit Rana, Kraak L, Pandey S, Bender M, Fitzgerald B, Hedden L, Fiske K, Taylor G, Wright A, Mehta I, Rahman S, Galipeau H, Mullett S, Gelhaus S, Watkins S, Bercik P, Nice T, Jabri B, Meisel M, Das J, Dermody T, Verdú E, Hinterleitner R

Immunity 2023

Stability and heterogeneity in the antimicrobiota reactivity of human milk-derived immunoglobulin A

Johnson-Hence C, Gopalakrishna K, Bodkin D, Coffey K, Burr A, Rahman S, Rai A, Abbott D, Sosa Y, Tometich J, Das J, Hand T

Journal of Experimental Medicine 2023

Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity

Li D, Jawale C, Zhou C, Lin L, Trevejo-Nunez G, Rahman S, Mullet S, Das J, Wendell S, Delgoffe G, Lionakis M, Gaffen S, Biswas P, Dubey S, Eichberg M

Cell Host & Microbe 2022

Functional reprogramming of monocytes in acute and convalescent severe COVID-19 patients

Brauns E, Azouz A, Grimaldi D, Xiao H, Thomas S, Nguyen M, Olislagers V, Vu Duc I, Orte Cano C, Del Marmol V, Pannus P, Libert F, Saussez S, Dauby N, Das J, Marchant A, Goriely S

JCI Insight 2022

Mechanisms of Impaired Lung Development and Ciliation in Mannosidase-1-Alpha-2 Mutants

Ningappa N, Adenuga N, Ngo K, Mohamed N, Narayanan T, Prasadan K, Ashokkumar C, Das J, Schmitt L, Hartman H, Sehrawat A, Salgado C, Reyes-Mugica M, Gittes G, Lo C, Subramaniam S, Sindhi R

Frontiers in Physiology 2021

Latency reversal agents modulate HIV antigen processing and presentation to CD8 T cells

Boucau J*, Das J*, Joshi N*, Le Gall S

PLoS Pathogens 2020

Genetic polymorphisms in the open reading frame of the CCR5 gene from HIV-1 seronegative and seropositive individuals from national capital regions of India

Ronsard L, Sood V, Yousif A.S, Ramesh J, Shankar V, Das J, Sumi N, Rai T, Mohankumar K, Sridharan S, Dorschel A, Ramachandran V.G, Banerjea A.C

Scientific Reports 2019

A multi-landing pad DNA integration platform for mammalian cell engineering

Gaidukov L, Wroblewska L, Teague B, Nelson T, Zhang X, Liu Y, Jagtap K, Mamo S, Tseng W, Lowe A, Das J, Bandara K, Baijuraj S, Summers N, Lu T, Zhang L, Weiss R

Nucleic Acids Research 2018

The transcription factors Runx3, T-bet and ThPOK co-regulate acquisition of cytotoxic function by human Th1 lymphocytes

Serroukh Y, Gu-Trantien C, Hooshiar Kashani B, Defrance M, Vu Manh T, Azouz A, Detavernier A, Hoyois A, Das J, Bizet M, Pollet E, Tabbuso T, Calonne E, van Gisbergen K, Dalod M, Fuks F, Goriely S, Marchant A

eLife 2018

Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data

Osorio D, Capasso A, Eckhardt S, Giri U, Somma A, Pitts T, Lieu C, Messersmith W, Bagby S, Singh H, Das J, Sahni N, Yi S, Kuijjer M

Nature Computational Science 2024

Landscape of microRNA regulatory network architecture and functional rerouting in cancer

Hua X, Li Y, Pentaparthi SR, McGrail DJ, Zou R, Guo L, Shrawat A, Cirillo KM, Li Q, Bhat A, Xu M, Qi D, Singh A, McGrath F, Andrews S, Aung KL, Das J, Zhou Y, Lodi A, Mills GB, Eckhardt SG, Mendillo ML, Tiziani S, Wu E, Huang JH, Sahni N, Yi SS

Cancer Research 2023

Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3

Grebinoski S, Zhang Q, Cillo AR, Manne S, Xiao H, Brunazzi EA, Tabib T, Cardello C, Lian CG, Murphy GF, Lafyatis R, Wherry EJ, Das J, Workman CJ, Vignali DAA

Nature Immunology 2022

Integrative annotation of variants from 1,092 humans- application to cancer genomics

Khurana E, Fu Y, Colonna V, Mu X.J, Kang H, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani U, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş Z, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin S, MacArthur D, Marth G, Muzny D, Pers T, Ritchie G, Rosenfeld J, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis E, Yu H, Rubin M, Tyler-Smith C, Gerstein M

Science 2013

Uncovering cell-type-specific immunomodulatory variants and molecular phenotypes in COVID-19 using structurally resolved protein networks

Chhibbar P*, Roy P*, Harioudh M*, McGrail D, Yang D, Singh H, Hinterleitner R, Gong YN, Yi SS, Sahni N, Sarkar S, Das J✝

Cell Reports 2024

Interpretable machine learning uncovers epithelial transcriptional rewiring and a role for Gelsolin in COPD

Sui J*, Xiao H*, Mbaekwe U, Ting NC, Murday K, Hu Q, Gregory AD, Kapellos TS, Yildirim AÖ, Königshoff M, Zhang Y, Sciurba FC, Das J✝, Kliment C✝

The Journal of Clinical Investigation Insight 2024

Spatial microniches of IL-2 combine with IL-10 to drive lung migratory TH2 cells in response to inhaled allergen

He K, Xiao H, MacDonald WA, Mehta I, Kishore A, Vincent A, Xu Z, Ray A, Chen W, Weaver CT, Lambrecht BN, Das J, Poholek AC

Nature Immunology 2024

Deep humoral profiling coupled to interpretable machine learning unveils diagnostic markers and pathophysiology of schistosomiasis

Saha A*, Chakraborty T*, Rahimikollu J, Xiao H, de Oliveira LBP, Hand TW, Handali S, Secor WE, A OFraga L, Fairley JK✝, Das J✝, Sarkar A✝

Science Translational Medicine 2024

Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics

Chávez R, Fili M, Han C, Rahman S, Bicar I, Gregory S, Helverson A, Hu G, Darbro B, Das J, Brown G, Haim H

PLoS Computational Biology 2024

Transcriptomic and Proteomic Characterization of the Immune Response to Elective Spinal Reconstructive Surgery -Impact of Aging and Comparison with Traumatic Injury Response

Bonaroti J, Ozel M,Chen T, Darby J, Sun X, Moheimani H, Reitz K, Kar U Zuckerbraun B,Das J,Okonkwo D, Billiar T

Journal of the American College of Surgeons 2024

SLIDE- Significant Latent factor Interaction Discovery and Exploration across biological domains

Rahimikollu J*, Xiao H*, Rosengart A, Rosen A, Tabib T, Zdinak P, He K, Bing X, Bunea F, Wegkamp M, Poholek A✝, Joglekar A✝, Lafyatis R✝, Das J✝

Nature Methods 2024

From bench to bedside via bytes- multi-omic immunoprofiling and integration using machine learning and network approaches

Xiao H*, Rosen A*, Chhibbar P*, Moise L, Das J✝

Human Vaccines & Immunotherapeutics 2023

Cell‐type‐specific biomarkers of systemic sclerosis disease severity capture cell‐intrinsic and cell‐extrinsic circuits

Berkowitz J*, Tabib T*, Xiao H, Sadej GM, Khanna D, Fuschiotti P, Lafyatis R✝, Das J✝

Arthritis and Rheumatology 2023

Determining asthma endotypes and outcomes- Complementing existing clinical practice with modern machine learning

Ray A*, Wenzel S* , Das J*

Cell Reports Medicine 2022

Lipidomic signatures align with inflammatory patterns and outcomes in critical illness

Wu J, Cyr A, Danielle G, Lovelace T, Panayiotis B, Das J, Kar U, Chen T, Guyette F, Yazer M, Daley B, Miller R, Harbrecht B, Claridge J, Phelan H, Zuckerbraun B, Neal M, Johansson P, Stensballe J, Namas R, Vodovotz Y, Sperry J

Nature Communications 2022

High Dimensional Multiomics Reveals Unique Characteristics of Early Plasma Administration in Polytrauma Patients With TBI

Wu J✝, Moheimani H, Li S, Kar U, Bonaroti J, Miller R, Daley B, Harbrecht B, Claridge J, Gruen D, Phelan H,Guyette F, Neal M, Das J✝, Sperry J, Billiar T✝

Annals of Surgery 2022

Multi-Omic Admission-Based Prognostic Biomarkers Identified by Machine Learning Algorithms Predict Patient Recovery and 30-Day Survival in Trauma Patients

Abdelhamid SS, Scioscia J, Vodovotz Y, Wu J, Rosengart A, Sung E, Rahman S, Voinchet R, Bonaroti J, Li S, Darby JL, Kar UK, Neal MD, Sperry J, Das J✝, Billiar TR✝

Metabolites 2022

A Supervised Take on Dimensionality Reduction via Hybrid Subset Selection

Rahimikollu J, Das J✝

Patterns 2022

Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3

Grebinoski S, Zhang Q, Cillo AR, Manne S, Xiao H, Brunazzi EA, Tabib T, Cardello C, Lian CG, Murphy GF, Lafyatis R, Wherry EJ, Das J, Workman CJ, Vignali DAA

Nature Immunology 2022

Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19

Peddireddy SP*, Rahman S*, Cillo AR, Vijay GM, Somasundaram A, Workman CJ, Bain W, McVerry BJ, Methe B, Lee JS, Ray P, Ray A, Bruno TC, Vignali DAA, Kitsios GD, Morris A, Singh H✝, Sarkar A✝, Das J✝

Cell Reports 2022

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

Bing X, Lovelace T, Bunea F, Wegkamp M, Kasturi S.P, Singh H✝, Benos P.V✝, Das J✝

Patterns 2022

A network-based approach to identify expression modules underlying rejection in pediatric liver transplantation

Ningappa M*, Rahman S*, Higgs B.W, Ashokkumar C.S, Sahni N, Sindhi R✝, Das J✝

Cell Reports Medicine 2022

People critically ill with COVID-19 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 lung viral burden

Cillo A, Somasundaram A, Shan F, Cardello C, Workman C, Kitsios G, Ruffin A, Kunning S, Lampenfeld C, Onkar S, Grebinoski S, Deshmukh G, Methe B, Liu C, Nambulli S, Andrews L, Duprex W, Joglekar A, Benos P, Ray P, Ray A, McVerry B, Zhang Y, Lee J, Das J, Singh H, Morris A, Bruno T, Vignali D

Cell Reports Medicine 2021

Delayed fractional dosing with RTS, S/AS01 improves humoral immunity to malaria via a balance of polyfunctional NANP6-and Pf16-specific antibodies

Das J*, Fallon J K*, Yu T C*, Michell A, Suscovich T J, Linde C, Natarajan H, Weiner J, Coccia M, Gregory S, Ackerman M E, Bergmann-Leitner E, Fontana L, Dutta S, Lauffenburger D A, Jongert E, Wille-Reece U, Alter G

Med 2021

Mining for humoral correlates of HIV control and latent reservoir size

Das J*, Devadhasan A, Linde C, Broge T, Sassic J, Mangano M, O Keefe S, Suscovich TJ, Streeck H, Irrinki A, Pohlmeyer C, Min-Oo G, Lin S, Weiner JA, Cihlar T, Ackerman ME, Julg B, Deeks S, Lauffenburger D, Alter G

PLOS Pathogens 2020

Mapping functional humoral correlates of protection against malaria challenge following RTS, S/AS01 vaccination

Suscovich T*, Fallon J*, Das J*, Demas A*, Crain J, Linde C, Michell A, Natarajan H, Arevalo C, Broge T, Linnekin T, Kulkarni V, Lu R, Luedemann C, Marquette M, March S, Weiner JA, Zavala F, Gregory S, Coccia M, Flores-Garcia Y, Ackerman ME, Bergmann-Leitner E, Lauffenburger D, Hendriks J, Sadoff J, Bhatia S, Jongert E, Wilke-Reece U, Alter G

Science Translational Medicine 2020

Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis

Weichselbaum L, Azouz A, Smolen K, Das J, Splittgerber M, Lepida A, Moreno C, Schreiber J, Serste T, Trepo E, Libert F, Gustot T, Goriely S

Journal of Hepatology 2020

Antibiotics-driven gut microbiome perturbation alters immunity to vaccine in humans

Hagan T, Cortese M, Rouphael N, Boudreau C, Linde C, Maddur M, Das J, Wang H, Guthmiller J, Zheng N, Huang M, Uphadhyay A, Gardinassi L, Petitdemange C, McCullough M, Johnson S, Gill K, Cervasi B, Zou J, Bretin A, Hahn M, Gewirtz A, Bosinger S, Wilson P, Li S, Alter G, Khurana S, Golding H, Pulendran B

Cell 2019

Latent model-based clustering for biological discovery

Bin X, Bunea F✝, Royer M, Das J✝

iScience 2019

Initiation of anti-retroviral therapy before pregnancy reduces the risk of infection related hospitalization in HIV-exposed uninfected infants

Goetghebuer T*, Smolen K*, Adler C*, Das J*, McBride T, Smits G, Lecomte S, Haelterman E, Barlow P, Piedra PA, van der Klis F, Kollmann TR, Lauffenburger DA, Alter G, Levy J, Marchant A

Clinical Infectious Diseases 2018

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

Miller-Novak L, Das J, Musich T, Demberg T, Weiner J, Venzon D, Mohanram V, Vargas-Inchaustegui D, Tuero I, Ackerman M, Alter G, Robert-Guroff M

Journal of Virology 2018

Route of immunization defines multiple mechanisms of vaccine-mediated protection against SIV

Ackerman M*, Das J*, Pittala S*, Broge T, Linde C, Suscovich T, Brown E, Bradley T, Natarajan H, Lin S, Sassic J, OKeefe S, Mehta N, Goodman D, Sips M, Weiner J, Tomaras G, Haynes B, Lauffenburger D, Bailey-Kellogg C, Roederer M, Alter G

Nature Medicine 2018

Mutation3D-cancer gene prediction through atomic clustering of coding variants in the structural proteome

Meyer M, Lapcevic R, Romero A, Yoon M, Das J, Beltrán J, Mort M, Stenson P, Cooper D, Paccanaro A, Yu H

Human Mutation 2016

ENCAPP-elastic-net-based prognosis prediction and biomarker discovery for human cancers

Das J*, Gayvert K*, Bunea F, Wegkamp M, Yu H

BMC Genomics 2015

Predicting cancer prognosis using functional genomics datasets

Das J*, Gayvert K*, Yu H

Cancer Informatics 2014

Uncovering cell-type-specific immunomodulatory variants and molecular phenotypes in COVID-19 using structurally resolved protein networks

Chhibbar P*, Roy P*, Harioudh M*, McGrail D, Yang D, Singh H, Hinterleitner R, Gong YN, Yi SS, Sahni N, Sarkar S, Das J✝

Cell Reports 2024

PRMT blockade induces defective DNA replication stress response and synergizes with PARP inhibition

Li H, Dobrolecki L, Sallas C, Zhang X, Kerr T, Bisht D, Wang Y, Awasthi S, Kaundal B, Wu S, Peng W, Mendillo M, Lu Y, Jeter C, Peng G, Liu J, Westin S, Sood A, Lewis M, Das J, Yi S, Bedford M, McGrail D, Sahni N

Cell Reports Medicine 2023

From bench to bedside via bytes- multi-omic immunoprofiling and integration using machine learning and network approaches

Xiao H*, Rosen A*, Chhibbar P*, Moise L, Das J✝

Human Vaccines & Immunotherapeutics 2023

High dimensional proteomics identifies organ injury patterns associated with outcomes in human trauma

Li SR, Moheimani H, Herzig B, Kail M, Krishnamoorthi N, Wu J, Abdelhamid S, Scioscia J, Sung E, Rosengart A, Bonaroti J, Johansson, P, Stensballe J, Neal M, Das J, Kar U, Sperry J, Billiar TR

Journal of Trauma and Acute Care Surgery 2023

A network-based approach to identify expression modules underlying rejection in pediatric liver transplantation

Ningappa M*, Rahman S*, Higgs B.W, Ashokkumar C.S, Sahni N, Sindhi R✝, Das J✝

Cell Reports Medicine 2022

Extracellular Matrix Injury of Kidney Allografts in Antibody-Mediated Rejection- A Proteomics Study

Clotet-Freixas S, McEvoy C, Batruch I, Pastrello C, Kotlyar M, Van J, Arambewela M, Boshart A, Farkona S, Niu Y, Li Y, Famure O, Bozovic A, Kulasingam V, Chen P, Kim J, Chan E, Moshkelgosha S, Rahman S, Das J, Martinu T, Juvet S, Jurisica I, Chruscinski A, John R, Konvalinka A

The Journal Of American Society of Nephrology 2020

Glucosylation by the Legionella effector SetA promotes the nuclear localization of the transcription factor TFEB

Beck W, Kim D, Das J, Yu H, Marcus B, Smolka M, Mao Y

iScience 2020

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

Fragoza R*, Das J*, Wierbowski S, Liang J, Tran T, Liang S, Beltran J, Rivera-Erick C, Ye K, Wang T, Yao L, Mort M, Stenson P, Cooper D, Wei X, Keinan A, Schimenti J, Clark A, Yu H

Nature Communications 2019

Effect of dietary fat and sucrose consumption on cardiac fibrosis in mice and rhesus monkeys

Natarajan N, Vujic A, Das J, Wang A, Phu K, Kiehm S, Ricci-Blair E, Zhu A,Vaughan K, Colman R, Mattison J, Lee R

JCI Insight 2019

Mutation3D-cancer gene prediction through atomic clustering of coding variants in the structural proteome

Meyer M, Lapcevic R, Romero A, Yoon M, Das J, Beltrán J, Mort M, Stenson P, Cooper D, Paccanaro A, Yu H

Human Mutation 2016

A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human

Vo T*, Das J*, Meyer M*, Cordero N, Akturk N, Wei X, Fair B, Degatano A, Fragoza R, Liu L, Matsuyama A, Trickey M, Horibata S, Grimson A, Yamano H, Yoshida M, Roth F, Pleiss J, Xia Y, Yu H

Cell 2016

Studying autism in context

Das J*, Meyer M*, Yu H

Cell Systems 2015

Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replication

de Oliviera F, Kim D, Cussiol J, Das J, Jeong M, Doerfler L, Schmidt K, Yu H, Smolka M

Molecular Cell 2015

A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations

Wei X*, Das J*, Fragoza R*, Liang J*, Bastos de Oliveira F, Lee H, Wang X, Mort M, Stenson P, Cooper D, Lipkin S, Smolka M, Yu H

PLoS Genetics 2014

Exploring mechanisms of human disease through structurally-resolved protein interactome networks

Das J*, Fragoza R, Lee H, Cordero N, Guo Y, Meyer M, Vo T, Wang X, Yu H

Molecular BioSystems 2014

Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks

Das J, Lee H, Sagar A, Fragoza R, Liang J, Wei X, Wang X, Mort M, Stenson P, Cooper D, Yu H

Human Mutation 2014

Dissecting disease inheritance modes in a 3D protein network challenges the guilt-by-association principle

Guo Y, Wei X, Das J, Grimson A, Lipkin S, Clark A, Yu H

American Journal of Human Genetics 2013

INstruct - a database of high-quality 3D structurally resolved protein interactome networks

Meyer M*, Das J*, Wang X*, Yu H

Bioinformatics 2013

Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways

Das J*, Vo T*, Wei X, Mellor J.C, Tong V, Degatano A, Wang X, Wang L, Cordero N, Kruer-Zerhusen N, Matsuyama A, Pleiss J, Lipkin S, Yoshida M, Roth F, Yu H

Science Signaling 2013

HINT:High quality interactomes and their applications in understanding human disease

Das J*, Yu H

BMC Systems Biology 2012

Genome-scale analysis of interaction dynamics reveals organization of biological networks

Das J*, Mohammed J*, Yu H

Bioinformatics 2012

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

Wang X*, Wei X*, Thijssen B*, Das J*, Lipkin S, Yu H

Nature Biotechnology 2012

Uncovering cell-type-specific immunomodulatory variants and molecular phenotypes in COVID-19 using structurally resolved protein networks

Cell Reports 2024

Interpretable machine learning uncovers epithelial transcriptional rewiring and a role for Gelsolin in COPD

The Journal of Clinical Investigation Insight 2024

Spatial microniches of IL-2 combine with IL-10 to drive lung migratory TH2 cells in response to inhaled allergen

Nature Immunology 2024

Deep humoral profiling coupled to interpretable machine learning unveils diagnostic markers and pathophysiology of schistosomiasis

Science Translational Medicine 2024

Tim-3 Is Required for Regulatory T Cell–Mediated Promotion of T Cell Exhaustion and Viral Persistence during Chronic Lymphocytic Choriomeningitis Virus Infection

Journal of Immunology 2024

High-dimensional profiling of immune responses to kidney transplant reveals heterogeneous T helper 1 and B cell effectors associated with rejection

American Journal of Transplantation 2024

Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics

PLoS Computational Biology 2024

Aberrant mitochondrial DNA synthesis in macrophages exacerbates inflammation and atherosclerosis

Nature Communications 2024

The RNA binding protein Arid5a drives IL-17-dependent autoantibody-induced glomerulonephritis

Journal of Experimental Medicine 2024

Temporal dynamics and genomic programming of plasma cell fates

Nature Immunology 2024

Transcriptomic and Proteomic Characterization of the Immune Response to Elective Spinal Reconstructive Surgery -Impact of Aging and Comparison with Traumatic Injury Response

Journal of the American College of Surgeons 2024

Regulatory T Cell Insufficiency in Autoimmune Diabetes Is Driven by Selective Loss of Neuropilin-1 on Intraislet Regulatory T Cells

Nature Computational Science 2024

Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data

Nature Computational Science 2024

SLIDE- Significant Latent factor Interaction Discovery and Exploration across biological domains

Nature Methods 2024

PRMT blockade induces defective DNA replication stress response and synergizes with PARP inhibition

Cell Reports Medicine 2023

SARS-CoV-2 mRNA vaccines induce greater complement activation and decreased viremia and Nef antibodies in men with HIV-1

The Journal of Infectious Diseases 2023

From bench to bedside via bytes- multi-omic immunoprofiling and integration using machine learning and network approaches

Human Vaccines & Immunotherapeutics 2023

The gut protist Tritrichomonas arnold restrains virus-mediated loss of oral tolerance by modulating dietary antigen-presenting dendritic cells

Immunity 2023

Stability and heterogeneity in the antimicrobiota reactivity of human milk-derived immunoglobulin A

Journal of Experimental Medicine 2023

High dimensional proteomics identifies organ injury patterns associated with outcomes in human trauma

Journal of Trauma and Acute Care Surgery 2023

Cell‐type‐specific biomarkers of systemic sclerosis disease severity capture cell‐intrinsic and cell‐extrinsic circuits

Arthritis and Rheumatology 2023

Antibodies against the Ebola virus soluble glycoprotein are associated with long-term vaccine-mediated protection of non-human primates

Cell Reports Medicine 2023

Landscape of microRNA regulatory network architecture and functional rerouting in cancer

Cancer Research 2023

Determining asthma endotypes and outcomes- Complementing existing clinical practice with modern machine learning

Cell Reports Medicine 2022

Lipidomic signatures align with inflammatory patterns and outcomes in critical illness

Nature Communications 2022

High Dimensional Multiomics Reveals Unique Characteristics of Early Plasma Administration in Polytrauma Patients With TBI

Annals of Surgery 2022

Multi-Omic Admission-Based Prognostic Biomarkers Identified by Machine Learning Algorithms Predict Patient Recovery and 30-Day Survival in Trauma Patients

Metabolites 2022

A Supervised Take on Dimensionality Reduction via Hybrid Subset Selection

Patterns 2022

Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3

Nature Immunology 2022

Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19

Cell Reports 2022

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

Patterns 2022

A network-based approach to identify expression modules underlying rejection in pediatric liver transplantation

Cell Reports Medicine 2022

Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity

Cell Host & Microbe 2022

Functional reprogramming of monocytes in acute and convalescent severe COVID-19 patients

JCI Insight 2022

Upper and lower respiratory tract correlates of protection against respiratory syncytial virus following vaccination of nonhuman primates

Cell Host Microbe 2022

People critically ill with COVID-19 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 lung viral burden

Cell Reports Medicine 2021

Delayed fractional dosing with RTS, S/AS01 improves humoral immunity to malaria via a balance of polyfunctional NANP6-and Pf16-specific antibodies

Med 2021

Mechanisms of Impaired Lung Development and Ciliation in Mannosidase-1-Alpha-2 Mutants

Frontiers in Physiology 2021

Extracellular Matrix Injury of Kidney Allografts in Antibody-Mediated Rejection- A Proteomics Study

The Journal Of American Society of Nephrology 2020

Mining for humoral correlates of HIV control and latent reservoir size

PLOS Pathogens 2020

Glucosylation by the Legionella effector SetA promotes the nuclear localization of the transcription factor TFEB

iScience 2020

Mapping functional humoral correlates of protection against malaria challenge following RTS, S/AS01 vaccination

Science Translational Medicine 2020

Co-immunization of DNA and Protein in the Same Anatomical Sites Induces Superior Protective Immune Responses against SHIV Challenge

Cell Reports 2020

Latency reversal agents modulate HIV antigen processing and presentation to CD8 T cells

PLoS Pathogens 2020

Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis

Journal of Hepatology 2020

Antibody Fc-glycosylation discriminates latent and active tuberculosis

The Journal of Infectious Diseases 2020

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

Nature Communications 2019

Antibiotics-driven gut microbiome perturbation alters immunity to vaccine in humans

Cell 2019

Effect of dietary fat and sucrose consumption on cardiac fibrosis in mice and rhesus monkeys

JCI Insight 2019

Fc glycan-mediated regulation of placental antibody transfer

Cell 2019

Genetic polymorphisms in the open reading frame of the CCR5 gene from HIV-1 seronegative and seropositive individuals from national capital regions of India

Scientific Reports 2019

Latent model-based clustering for biological discovery

iScience 2019

Initiation of anti-retroviral therapy before pregnancy reduces the risk of infection related hospitalization in HIV-exposed uninfected infants

Clinical Infectious Diseases 2018

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

Journal of Virology 2018

Route of immunization defines multiple mechanisms of vaccine-mediated protection against SIV

Nature Medicine 2018

A role for Fc function in therapeutic monoclonal antibody-mediated protection against Ebola virus

Cell Host Microbe 2018

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

Journal of Virology 2018

A multi-landing pad DNA integration platform for mammalian cell engineering

Nucleic Acids Research 2018

The transcription factors Runx3, T-bet and ThPOK co-regulate acquisition of cytotoxic function by human Th1 lymphocytes

eLife 2018

Temporal variation in HIV-specific IgG subclass antibodies during acute infection differentiates spontaneous 4 controllers from chronic progressors

AIDS 2018

Mutation3D-cancer gene prediction through atomic clustering of coding variants in the structural proteome

Human Mutation 2016

A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human

Cell 2016

Studying autism in context

Cell Systems 2015

Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replication

Molecular Cell 2015

ENCAPP-elastic-net-based prognosis prediction and biomarker discovery for human cancers

BMC Genomics 2015

A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations

PLoS Genetics 2014

Predicting cancer prognosis using functional genomics datasets

Cancer Informatics 2014

Exploring mechanisms of human disease through structurally-resolved protein interactome networks

Molecular BioSystems 2014

Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks

Human Mutation 2014

Dissecting disease inheritance modes in a 3D protein network challenges the guilt-by-association principle

American Journal of Human Genetics 2013

INstruct - a database of high-quality 3D structurally resolved protein interactome networks

Bioinformatics 2013

Integrative annotation of variants from 1,092 humans- application to cancer genomics

Science 2013

Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways

Science Signaling 2013

HINT:High quality interactomes and their applications in understanding human disease

BMC Systems Biology 2012

Genome-scale analysis of interaction dynamics reveals organization of biological networks

Bioinformatics 2012

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

Nature Biotechnology 2012