Publications

Total: 50 published papers; 2 currently under review/in revision

Under review/in revision (2)

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Hua X., Li Y., Pentaparthi S., Guo L., McGrail D., Bhat A., Zou R., Xu M., Qi D., Singh A., McGrath F., Huang J., Andrews S., Wu E., Das J., Zhou Y., Sahni N., Yi SS.

bioRxiv

doi

Mahajan V. S., Rahman S. A., Viswanadham V. V. , Yuen G. J., Sun N., Mattoo H., Pillai S. S., Das J^.

bioRxiv

doi

 

2022 (9)

Peddireddy SP, Rahman SA, 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, 39(13), 111020.

doi   PMID:35738278

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A Supervised Take on Dimensionality Reduction via Hybrid Subset Selection

Rahimikollu J., Das J^.

Patterns (Cell Press), In Press

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High Dimensional Multi-omics 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, In Press

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Grebinoski S., Zhang Q., Cillo A., Manne S., Xiao H., Brunazzi E., Tabib T., Cardello C., Lian C., Murphy G., Lafyatis R., E. Wherry J., Das J., Workman C., Vignali D, 

Nature Immunology, 23(6): 868-877

doi   PMID: 35618829

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Ningappa, M., Rahman, S. A., Higgs, B. W., Ashokkumar, C. S., Sahni, N., Sindhi, R., & Das, J^.

Cell Reports Medicine, 3(4), 100605.

doi    PMID: 35492246

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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 7(9) 

doi    PMID: 35380990

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

Cell Host & Microbe, 30(4), 530-544.

doi    PMID: 35316647

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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 (Cell Press) 3(5):100473.

doi    PMID: 35607614

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

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

Cell Host & Microbe, 30(1), 41-52.

doi    PMID: 34879230

 

2021 (3)

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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 . 12:658518. 

doi    PMID: 34366878

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

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

Cell Reports Medicine, 2(12), 100476.

doi    PMID: 34873589

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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 (Cell Press), 2(11), 1269-1286.

doi    PMID: 35590199

2020 (8)

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Das J., Devadhasan A., Linde C., Broge T., Sassic J., Mangano M., O’ Keefe S., Suscovich T.J., Streeck H., Irrinki A., Pohlmeyer C., Min-Oo G., Lin S., Weiner J.A., Cihlar T., Ackerman M.E., Julg B., Deeks S., Lauffenburger D., Alter G.

PLoS Pathogens 16(10):e1008868

doi    PMID: 33048992

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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.

Journal of the American Society of Nephrology 31(11): 2705-2724

doi    PMID: 32900843

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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 (Cell Press), 101300

doi    PMID: 32622269

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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 31(6): 107624

doi    PMID: 32402293​​

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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 J.A., Zavala F., Gregory S., Coccia M., Flores-Garcia Y., Ackerman M.E., Bergmann-Leitner E., Lauffenburger D., Hendriks J., Sadoff J., Bhatia S., Jongert E., Wilke-Reece U., Alter G..

Science Translational Medicine ;12(553):eabb4757

doi    PMID: 32718991​​

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

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

PLoS Pathogens ;16(3):e1008442.

doi    PMID: 32196533​​​

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Antibody Fc-glycosylation discriminates latent and active tuberculosis

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

Journal of Infectious Diseases; 222(12), 2093-2102.

doi    PMID: ​​​​ 32060529

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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; 73(2): 303-314 

doi    PMID: ​​​​ 32145259

 
 
 

2019 (6)

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Bin X., Bunea F., Royer M., Das J.^.

 iScience (Cell Press) 14:125-135

doi    PMID: ​​​​ 30954780

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

Natarajan N., Vujic A., Das J., Wang A.C., Phu K.K., Kiehm S.H., Ricci-Blair E.M., Zhu A.Y., Vaughan K.L., Colman R.J., Mattison J.A., Lee R.T..

 Journal of Clinical Investigation Insight 4(18):e128685

doi    PMID: ​​​​ 31415241

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

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

Nature Communications ; 10(1):1-15

doi    PMID: ​​​​ 31515488​​

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Fc glycan-mediated regulation of placental antibody transfer

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

 Cell 178(1):190-201

doi    PMID: ​​​​ 31204102​​

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

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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 9(1):7594

doi    PMID: ​​​​ 31110236​​

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

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

Cell ; 178(6): 1313-1328

doi    PMID: ​​​​ 31491384​​

 

2018 (8)

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

Clinical Infectious Diseases 68(7): 1193-1203

doi    PMID: ​​​​ 30215689​​

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

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

Cell Host & Microbe 24(2):221-233.

doi    PMID: ​​​​ 30215689​​

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

Ackerman M.^, Das J., Pittala S., Broge T., Linde C., Suscovich T.J., Brown E.P., Bradley T., Natarajan H., Lin S., Sassic J.K., O'Keefe S., Mehta N., Goodman D., Sips M., Weiner J.A., Tomaras G.D., Haynes B.F., Lauffenburger D.A., Bailey-Kellogg C., Roederer M., Alter G.

Nature Medicine 24(10):1590-1598

doi    PMID: ​​​​ 30215689​​

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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.P., 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 7: e30496.

doi    PMID: ​​​​ 29488879​​​

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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.A., Demberg T., Weiner J.A., Venzon D.J., Mohanram V., Vargas-Inchaustegui D.A., Tuero I., Ackerman M.E., Alter G., Robert-Guroff M.

Journal of Virology 92(19): e00721-18.

doi    PMID: ​​​​ 30021899​​​

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

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

AIDS 32(4):443-450.

doi    PMID: ​​​​ 29239894​​​

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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.A., Lowe A., Das J., Bandara K., Baijuraj S., Summers N.M., Lu T.K., Zhang L., Weiss R.

Nucleic Acids Research 46(8): 4072-4086.

doi    PMID: ​​​​ 29617873​​​

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

Journal of Virology 92(15): pii: e00281-18.

doi    PMID: 29793957

2016 (2)

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

Cell, 164(1): 310-323.

doi    PMID: ​​​​ 26771498​​​

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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.F., Mort M., Stenson P.D., Cooper D.N., Paccanaro A., Yu H.

Human Mutation 37(5): 447-456.

doi    PMID: ​​​​ 29617873​​​

 
 

2015 (3)

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

BMC Genomics 16: 263.

doi    PMID: ​​​​ 25887568​​​

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

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

Molecular Cell 57(6): 1124-1132.

doi    PMID: ​​​​ 25752575​​​

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Studying autism in context

Das J., Meyer M.J., Yu H.

Cell Systems 1(5): 312-313.

doi    PMID: ​​​​ 27136240​​​

2014 (4)

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

PLoS Genetics 10(12): e1004819.

doi    PMID: ​​​​ 25502805​​​

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

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

Human Mutation 35(5): 585-593.

doi    PMID: ​​​​ 24599843​​​

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

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

Molecular BioSystems 10(1): 9-17

doi    PMID: ​​​​ 24096645​​​

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Predicting cancer prognosis using functional genomics datasets

Das J., Gayvert K.M., Yu H.

Cancer Informatics Suppl. 5: 85-88.

doi    PMID: ​​​​ 25392695​​​

 
 

2013 (4)

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

Science Signaling 6, ra38. 

doi    PMID: ​​​​ 23695164​​​

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

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Khurana E., Fu Y., Colonna V., Mu X.J., Kang H.M., 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.S., Flicek P., Fragoza R., Garrison E., Gibbs R., Gümüş Z.H., Herrero J., Kitabayashi N., Kong Y., Lage K., Liluashvili V., Lipkin S.M., MacArthur D.G., Marth G., Muzny D., Pers T.H., Ritchie G.R.S., Rosenfeld J.A., Sisu C., Wei X., Wilson M., Xue Y., Yu F., Dermitzakis E.T., Yu H., Rubin M.A., Tyler-Smith C., Gerstein M.

Science 342 (6154), 1235587.

doi    PMID: ​​​​ 24092746​​​

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

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

Bioinformatics 29(12): 1577-1579.

doi    PMID: ​​​​ 23599502​​​

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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.M., Clark A.G., Yu H.

American Journal of Human Genetics 3(1):78-89.

doi    PMID: ​​​​ 23791107​​​

2012 (3)

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Das J. and Yu H.

BMC Systems Biology 6(1): 92.

doi    PMID: ​​​​ 22846459​​​

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

Das J., Mohammed J., Yu H.

Bioinformatics 28(14): 1873-1878.

doi    PMID: ​​​​ 22576179​​​

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

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

Nature Biotechnology 30(2): 159-164. 

doi    PMID: ​​​​ 22252508​​​