Publications
Under review/in revision (2)
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
Mahajan V. S., Rahman S. A., Viswanadham V. V. , Yuen G. J., Sun N., Mattoo H., Pillai S. S., Das J^.
bioRxiv
2022 (11)
Junru W, Anthony C, Danielle S. G, Tyler C. L, Panayiotis V. B, Jishnu Das, Upendra K. Kar, Tianmeng Chen, Francis X. Guyette, Mark H. Yazer, Brian J. Daley, Richard S. Miller, Brian G. Harbrecht, Jeffrey A. Claridge, Herb A. Phelan, Brian S. Zuckerbraun, Matthew D. Neal, Pär I. Johansson, Jakob Stensballe, Rami A. Namas, Yoram Vodovotz, Jason L. Sperry, Timothy R. Billiar & PAMPer study group
Nat Commun 13, 6789 (2022).
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 Oct; 276(4): 673-683
Ningappa, M., Rahman, S. A., Higgs, B. W., Ashokkumar, C. S., Sahni, N., Sindhi, R., & Das, J^.
Cell Reports Medicine, 3(4), 100605.
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)
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.
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.
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.
2021 (3)
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.
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.
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.
2020 (8)
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
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
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
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
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
Latency reversal agents modulate HIV antigen processing and presentation to CD8 T cells
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.
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
2019 (6)
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
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
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
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 9(1):7594
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
2018 (8)
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
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.
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
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.
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.
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.
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.
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)
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.
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.
2015 (3)
Das J., Gayvert K.M., Bunea F., Wegkamp M.H., Yu H.
BMC Genomics 16: 263.
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.
Studying autism in context
2014 (4)
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.
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.
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
Predicting cancer prognosis using functional genomics datasets
2013 (4)
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.
Integrative annotation of variants from 1,092 humans: application to cancer genomics
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.
INstruct: a database of high-quality 3D structurally resolved protein interactome networks
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.
2012 (3)
Genome-scale analysis of interaction dynamics reveals organization of biological networks
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.