Pramod Shinde
Associate Research Scientist in PathologyCards
About
Research
Publications
Featured Publications
Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality
Gygi J, Maguire C, Patel R, Shinde P, Konstorum A, Shannon C, Xu L, Hoch A, Jayavelu N, Haddad E, Network I, Reed E, Kraft M, McComsey G, Metcalf J, Ozonoff A, Esserman D, Cairns C, Rouphael N, Bosinger S, Kim-Schulze S, Krammer F, Rosen L, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier C, Steen H, Altman M, Montgomery R, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen K, Fragiadakis G, Becker P, Sekaly R, Ehrlich L, Fourati S, Peters B, Kleinstein S, Guan L. Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. Journal Of Clinical Investigation 2024, 134: e176640. PMID: 38690733, PMCID: PMC11060740, DOI: 10.1172/jci176640.Peer-Reviewed Original ResearchA multi-omics systems vaccinology resource to develop and test computational models of immunity
Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum J, Overton J, Guzman-Orozco H, Nili S, Orfield S, Gygi J, da Silva Antunes R, Sette A, Grant B, Olsen L, Konstorum A, Guan L, Ay F, Kleinstein S, Peters B. A multi-omics systems vaccinology resource to develop and test computational models of immunity. Cell Reports Methods 2024, 4: 100731. PMID: 38490204, PMCID: PMC10985234, DOI: 10.1016/j.crmeth.2024.100731.Peer-Reviewed Original ResearchImpact of modular mitochondrial epistatic interactions on the evolution of human subpopulations
Shinde P, Whitwell H, Verma R, Ivanchenko M, Zaikin A, Jalan S. Impact of modular mitochondrial epistatic interactions on the evolution of human subpopulations. Mitochondrion 2021, 58: 111-122. PMID: 33618020, DOI: 10.1016/j.mito.2021.02.004.Peer-Reviewed Original Research
2025
Brain rewiring during development: A comparative analysis of larval and adult Drosophila melanogaster connectomes
Yadav P, Shinde P, Singh A. Brain rewiring during development: A comparative analysis of larval and adult Drosophila melanogaster connectomes. Network Neuroscience 2025, 9: 1299-1322. PMID: 41280232, PMCID: PMC12635837, DOI: 10.1162/netn.a.26.Peer-Reviewed Original ResearchIs the vaccination-induced B cell receptor repertoire predictable?
Richardson E, Willemsen L, Shinde P, Nielsen M, Peters B. Is the vaccination-induced B cell receptor repertoire predictable? ImmunoInformatics 2025, 19: 100057. PMID: 41311460, PMCID: PMC12657037, DOI: 10.1016/j.immuno.2025.100057.Peer-Reviewed Original ResearchTh1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loop
Willemsen L, Lee J, Shinde P, Soldevila F, Aoki M, Orfield S, Kojima M, da Silva Antunes R, Sette A, Peters B. Th1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loop. Nature Communications 2025, 16: 3132. PMID: 40169665, PMCID: PMC11961675, DOI: 10.1038/s41467-025-58460-8.Peer-Reviewed Original ResearchPutting computational models of immunity to the test—An invited challenge to predict B.pertussis vaccination responses
Shinde P, Willemsen L, Anderson M, Aoki M, Basu S, Burel J, Cheng P, Dastidar S, Dunleavy A, Einav T, Forschmiedt J, Fourati S, Garcia J, Gibson W, Greenbaum J, Guan L, Guan W, Gygi J, Ha B, Hou J, Hsiao J, Huang Y, Jansen R, Kakoty B, Kang Z, Kobie J, Kojima M, Konstorum A, Lee J, Lewis S, Li A, Lock E, Mahita J, Mendes M, Meng H, Neher A, Nili S, Olsen L, Orfield S, Overton J, Pai N, Parker C, Qian B, Rasmussen M, Reyna J, Richardson E, Safo S, Sorenson J, Srinivasan A, Thrupp N, Tippalagama R, Trevizani R, Ventz S, Wang J, Wu C, Ay F, Grant B, Kleinstein S, Peters B. Putting computational models of immunity to the test—An invited challenge to predict B.pertussis vaccination responses. PLOS Computational Biology 2025, 21: e1012927. PMID: 40163550, PMCID: PMC11978014, DOI: 10.1371/journal.pcbi.1012927.Peer-Reviewed Original ResearchExploring Pertussis Vaccination Through Systems Vaccinology
Hsiao J, Shinde P, Willemsen L, Kojima M, Reyna J, Peters B, Grant B. Exploring Pertussis Vaccination Through Systems Vaccinology. CourseSource 2025, 12 DOI: 10.24918/cs.2025.3.Peer-Reviewed Original Research
2023
Higher-order co-mutation interactions in mitochondrial genomes
Verma R, Shinde P, Mishra A, Jalan S. Higher-order co-mutation interactions in mitochondrial genomes. New Journal Of Physics 2023, 25: 093021. DOI: 10.1088/1367-2630/acf51a.Peer-Reviewed Original Research
2022
Nucleotide-based genetic networks: Methods and applications
Verma R, Shinde P, Jalan S. Nucleotide-based genetic networks: Methods and applications. Journal Of Biosciences 2022, 47: 63. PMID: 36226367, PMCID: PMC9554864, DOI: 10.1007/s12038-022-00290-7.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements