Publications

Publications (peer reviewed)

Computational Models Predict Immunity
P. Shinde, L. Willemsen, M. Anderson, M. Aoki, S. Basu, J.G. Burel, P. Cheng, S.G. Dastidar, A. Dunleavy, T. Einav, B. Peters
PLoS Computational Biology ((invited challenge on B. pertussis)) 2025 [doi]
Media: [DOI]

Th1 Feedback in Vaccine Response
L. Willemsen, J. Lee, P. Shinde, F. Soldevila, M. Aoki, S. Orfield, M. Kojima, R.D.S. Antunes, A. Sette, B. Peters
Nature Communications ((study of B. pertussis polarization)) 2025 [doi]
Media: [Nature]

Predictable B Cell Repertoires
E. Richardson, L. Willemsen, P. Shinde, M. Nielsen, B. Peters
ImmunoInformatics ((modeling BCR repertoires)) 2025 [doi]

Multi-Omics Resource for Immunity
P. Shinde, F.C. Soldevila, J. Reyna, M. Kojima, J.A. Overton, B. Ha, J. Greenbaum, F. Ay, B.J. Grant, S.H. Kleinstein, B. Peters
Cell Reports Methods ((cover feature)) 2024 [doi]

Immune Programs in COVID-19 Severity
J. Gygi, C. Maguire, R. Patel, P. Shinde, A. Konstorum, C. Shannon, L. Xu, A. Hoch, N. Jayavelu, IMPACC Network, B. Peters, S.H. Kleinstein, L. Guan
Journal of Clinical Investigation ((multi-omics COVID-19 cohort)) 2024 [doi]

Exploring Pertussis via Systems Vaccinology
J. H., P. Shinde, L. Willemsen, M. Kojima, J. Reyna, B. Peters, B. Grant
CourseSource ((peer-reviewed teaching resource)) 2024 [doi]

Higher-Order Mitochondrial Co-Mutations
R.K. Verma, P. Shinde, A. Mishra, S. Jalan
New Journal of Physics 2023 [doi]

Nucleotide Genetic Network Methods
R.K. Verma, P. Shinde, S. Jalan
Journal of Biosciences 2022 [doi]

Mitochondrial Epistasis and Evolution
P. Shinde, H.J. Whitwell, R.K. Verma, A. Zaikin, S. Jalan
Mitochondrion 2022 [doi]

Mitochondrial Networks at High Altitude
R.K. Verma, A. Kalyakulina, C. Giuliani, P. Shinde, A.D. Kachhvah, M. Ivanchenko, S. Jalan
Scientific Reports 2021 [doi]

Symmetry in Cancer Networks
P. Shinde, L. Marrec, A. Rai, A. Yadav, R. Kumar, M. Ivanchenko, A. Zaikin, S. Jalan
Network Science 2019 [doi]

Network Spectra for Drug Targets
A. Rai, P. Shinde, S. Jalan
Applied Network Science 2018 [doi]

Codon Network Motifs in Mitochondria
P. Shinde, C. Sarkar, S. Jalan
Scientific Reports 2018 [doi]

Genetic Characterization of H1N1
D. Gohil, S. Kothari, P. Shinde, R. Meharunkar, R. Warke, A. Chowdhary, R. Deshmukh
Current Microbiology 2017 [doi]

Anti-Influenza Plant Extracts
R.D. Chavan, P. Shinde, K. Girkar, R. Madage, A. Chowdhary
Pharmacognosy Research 2016 [doi]

Multilayer Protein Network in Worms
P. Shinde, S. Jalan
Europhysics Letters 2015 [doi]

Drug Susceptibility of H3N2 Strains
D.J. Gohil, S.T. Kothari, P. Shinde, A.S. Chintakrindi, R. Meharunkar, R.V. Warke, M.A. Kanyalkar, A.S. Chowdhary, R.A. Deshmukh
Infection, Genetics and Evolution 2015 [doi]

Dissortativity in Oral Cancer Networks
P. Shinde, A. Yadav, A. Rai, S. Jalan
European Physical Journal B 2015 [doi]

Oseltamivir-Resistant H1N1 Characterization
D. Gohil, S. Kothari, P. Shinde, A.C. Krindi, R. Meharunkar, R. Warke, M. Kanyalkar, A. Chowdhary, R. Deshmukh
International Journal of Advanced Research 2015 [doi]

Oseltamivir-Resistant H1N1 Infection
D. Gohil, S. Kothari, P. Shinde, A.C. Krindi, R. Meharunkar, R. Warke, M. Kanyalkar, A. Chowdhary, R. Deshmukh
Journal of Antivirals & Antiretrovirals 2015 [doi]