Publications – PROTEOMICS LAB

4. From Proteins to Proteomics
Basic Concepts, Techniques, and Applications
Edited by: Sanjeeva Srivastava
Edition: 1st Edition
Published on: 2022
eBook published on: 29th December 2022
Publication location: Boca Raton
Imprint: CRC Press
doi: https://doi.org/10.1201/9781003098645
Pages: 272
eBook ISBN: 9781003098645
Subjects: Bioscience
Cite as: Srivastava, S. (2022). From Proteins to Proteomics: Basic Concepts, Techniques, and Applications (1st ed.). CRC Press. https://doi.org/10.1201/9781003098645

3. Multi-Pronged Omics Technologies to Understand COVID-19
Edited by: Sanjeeva Srivastava
Edition: 1st Edition
Published on: 2022
eBook published on: 7th July 2022
Publication location: Boca Raton
Imprint: CRC Press
doi: https://doi.org/10.1201/9781003220787
Pages: 236
eBook ISBN: 9781003220787
Subjects: Bioscience, Engineering & Technology
Cite as: Srivastava, S. (Ed.). (2022). Multi-Pronged Omics Technologies to Understand COVID-19 (1st ed.). CRC Press. https://doi.org/10.1201/9781003220787

2. Protein Microarrays for Disease Analysis
Methods and Protocols
Edited by: Rodrigo Barderas, Joshua LaBaer, Sanjeeva Srivastava
Edition: 1st Edition
Published on: 2021
eBook published on: 11th June 2021
Publication location: New York
Imprint: Humana Press New York, Springer Protocols
doi: https://doi.org/10.1007/978-1-0716-1562-1
Pages: XIV, 282
eBook ISBN: 978-1-0716-1562-1
Subjects: Protein Biochemistry
Cite as: Barderas, R., LaBaer, J., & Srivastava, S. (2021). Protein Microarrays for Disease Analysis. Humana Press. https://doi.org/10.1007/978-1-0716-1562-1

1. Biomarker Discovery in the Developing World: Dissecting the Pipeline for Meeting the Challenges
Edited by: Sanjeeva Srivastava
Edition: 1st Edition
Published on: 2016
eBook published on: 30th September 2016
Publication location: New Delhi
Imprint: Springer
doi: https://doi.org/10.1007/978-81-322-2837-0
Pages: XI, 118
eBook ISBN: 978-81-322-2837-0
Subjects: Cancer Biology, Protein Biochemistry, Diseases, Medical Microbiology
Cite as: Srivastava, S. (Ed.). (2016). Biomarker Discovery in the Developing World: Dissecting the Pipeline for Meeting the Challenges. Springer India. https://doi.org/10.1007/978-81-322-2837-0

164. Pai, M. G. J., Biswas, D., Verma, A., & Srivastava, S. (2023). A proteome-level view of brain tumors for a better understanding of novel diagnosis, prognosis, and therapy. Expert review of proteomics, 10.1080/14789450.2023.2283498. Advance online publication. https://doi.org/10.1080/14789450.2023.2283498

163. Nissa, M. U., Banerjee, A., Goswami, M., & Srivastava, S. (2022). Comprehensive data and workflow for mapping global proteome and post-translational modifications in Indian Major Carp, Labeo rohita. Data in brief, 45, 108746. https://doi.org/10.1016/j.dib.2022.108746

162. Biswas, D., Halder, A., Barpanda, A., Ghosh, S., Chauhan, A., Bhat, L., Epari, S., Shetty, P., Moiyadi, A., Ball, G. R., & Srivastava, S. (2023). Integrated Meta-Omics Analysis Unveils the Pathways Modulating Tumorigenesis and Proliferation in High-Grade Meningioma. Cells, 12(20), 2483. https://doi.org/10.3390/cells12202483

161. Rajoria, S., Nair, D., Suvarna, K., Pai, M. G. J., Salkar, A., Palanivel, V., Verma, A., Barpanda, A., Awasthi, G., Doshi, H., Dhara, V., Burli, A., Agrawal, S., Shrivastav, O., Shastri, J., & Srivastava, S. (2023). Proteomic Investigation of COVID-19 Severity During the Tsunamic Second Wave in Mumbai. Advances in experimental medicine and biology, 1412, 175–195. https://doi.org/10.1007/978-3-031-28012-2_9

160. Halder, A., Biswas, D., Chauhan, A., Saha, A., Auromahima, S., Yadav, D., Nissa, M. U., Iyer, G., Parihari, S., Sharma, G., Epari, S., Shetty, P., Moiyadi, A., Ball, G. R., & Srivastava, S. (2023). A large-scale targeted proteomics of serum and tissue shows the utility of classifying high grade and low grade meningioma tumors. Clinical proteomics, 20(1), 41. https://doi.org/10.1186/s12014-023-09426-9

159. Bihani, S., Gupta, A., Mehta, S., Rajczewski, A. T., Johnson, J., Borishetty, D., Griffin, T. J., Srivastava, S., & Jagtap, P. D. (2023). Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients. Journal of proteome research, 22(8), 2608–2619. https://doi.org/10.1021/acs.jproteome.3c00040

158. Sharma, G., Pund, S., Govindan, R., Nissa, M. U., Biswas, D., Middha, S., Ganguly, K., Anand, M. P., Banerjee, R., & Srivastava, S. (2023). A Proteomics Investigation of Cigarette Smoke Exposed Wistar Rats Revealed Improved Anti-Inflammatory Effects of the Cysteamine Nanoemulsions Delivered via Inhalation. Omics : a journal of integrative biology, 27(8), 338–360. https://doi.org/10.1089/omi.2023.0074

157. Biswas, D., Shenoy, S. V., Chauhan, A., Halder, A., Ghosh, B., Padhye, A., Auromahima, S., Yadav, D., Sasmal, S., Dutta, S., Kumari, N., Bhavaskar, H., Mukherjee, A. P., Kumar, T. R., & Srivastava, S. (2023). BrainProt(TM) 3.0: Understanding human brain diseases using comprehensively curated & integrated omics datasets. BrainProt(TM) 3.0: Understanding Human Brain Diseases Using Comprehensively Curated & Integrated OMICS Datasets. [PrePrint] https://doi.org/10.1101/2023.06.21.545851

156. Rajoria, S., Halder, A., Tarnekar, I., Pal, P., Bansal, P., & Srivastava, S. (2023). Detection of Mutant Peptides of SARS-CoV-2 Variants by LC/MS in the DDA Approach Using an In-House Database. Journal of proteome research, 22(6), 1816–1827.doi:10.1021/acs.jproteome.2c00819

155. Aggarwal, S., Karmakar, A., Krishnakumar, S., Paul, U., Singh, A., Banerjee, N., Laha, N., Roy Ball, G., & Srivastava, S. (2023). Advances in Drug Discovery based on Genomics, Proteomics and Bioinformatics in Malaria. Current topics in medicinal chemistry, 23(7), 551–578. doi:10.2174/1568026623666230418114455

154. Banerjee, A., Halder, A., Jadhav, P., Sarkar, A., Hole, A., Shastri, J. S., Agrawal, S., Chilakapati, M. K., & Srivastava, S. (2023). SARS-CoV-2 severity classification from plasma sample using confocal Raman spectroscopy. Journal of Raman spectroscopy : JRS, 54(1), 124–132. https://doi.org/10.1002/jrs.6461

153. Banerjee, A., Biswas, D., Barpanda, A., Halder, A., Sibal, S., Kattimani, R., Shah, A., Mahadevan, A., Goel, A., & Srivastava, S. (2023). The First Pituitary Proteome Landscape From Matched Anterior and Posterior Lobes for a Better Understanding of the Pituitary Gland. Molecular & cellular proteomics : MCP, 22(1), 100478. https://doi.org/10.1016/j.mcpro.2022.100478

152. Barpanda, A., Tuckley, C., Ray, A., Banerjee, A., Duttagupta, S. P., Kantharia, C., & Srivastava, S. (2023). A protein microarray-based serum proteomic investigation reveals distinct autoantibody signature in colorectal cancer. Proteomics. Clinical applications, 17(2), e2200062. https://doi.org/10.1002/prca.202200062

151. Biswas, D., Kumari, N., Lachén-Montes, M., Dutta, S., Agrawal, I., Samanta, D., Shenoy, S. V., Halder, A., Fernández-Irigoyen, J., Padhye, A. R., Santamaría, E., & Srivastava, S. (2023). Deep Phosphoproteome Landscape of Interhemispheric Functionality of Neuroanatomical Regions of the Human Brain. Journal of proteome research, 22(4), 1043–1055. https://doi.org/10.1021/acs.jproteome.2c00244

150. Aggarwal, S., Selvaraj, S., Subramanian, J. N., Vijayalakshmi, M. A., Patankar, S., & Srivastava, S. (2023). Polyclonal Antibody Generation against PvTRAg for the Development of a Diagnostic Assay for Plasmodium vivax. Diagnostics (Basel, Switzerland), 13(5), 835. https://doi.org/10.3390/diagnostics13050835

149. Ghantasala, S., Bhat, A., Agarwal, U., Biswas, D., Bhattarai, P., Epari, S., Moiyadi, A., & Srivastava, S. (2023). Deep proteome investigation of high-grade gliomas reveals heterogeneity driving differential metabolism of 5-aminolevulinic acid. Neuro-oncology advances, 5(1), vdad065. https://doi.org/10.1093/noajnl/vdad065

148. Ayushi Verma, Ankit Halder, Prasoon Prakash, Sanjeeva Srivastava, Chapter 3 – Identification of potential biomarkers in glioblastoma through omics technologies and big data analysis, New Insights Into Glioblastoma, Academic Press, 2023, Pages 33-54, ISBN 9780323998734, https://doi.org/10.1016/B978-0-323-99873-4.00008-6

147. Acharjee, Arup et al. “Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray.” Viruses vol. 15,1 248. 15 Jan. 2023, doi:10.3390/v15010248

146. Barpanda A, Halder A, Dhote A, Parihari S, Kantharia C, Srivastava S. Colon Adenocarcinoma Quantitative Proteomics Reveals Dysregulation in Key Cancer Signaling Pathways and a Candidate Protein Marker Panel. OMICS. 2023 Feb 1. doi: 10.1089/omi.2022.0169.

145. Barpanda, A., Biswas, D., Verma, A., Parihari, S., Singh, A., Kapoor, S., Kantharia, C. and Srivastava, S., 2023. Integrative Proteomic and Pharmacological Analysis of Colon Cancer Reveals the Classical Lipogenic Pathway with Prognostic and Therapeutic Opportunities. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00646

144. Rajoria, S., Nissa, M.U., Suvarna, K., Khatri, H. and Srivastava, S., 2023. Multiomics data analysis workflow to assess severity in longitudinal plasma samples of COVID-19 patients. Data in Brief, 46, p.108765. https://doi.org/10.1016/j.dib.2022.108765

143. Gupta, S., Manubhai, K.P., Mukherjee, S. and Srivastava, S., 2017. Serum profiling for identification of autoantibody signatures in diseases using protein microarrays. In Serum/Plasma Proteomics (pp. 303-315). Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7057-5_21 (Book Chapter)

142. Mukherjee, A., Pednekar, C.B., Kolke, S.S., Kattimani, M., Duraisamy, S., Burli, A.R., Gupta, S. and Srivastava, S., 2022. Insights on Proteomics-Driven Body Fluid-Based Biomarkers of Cervical Cancer. Proteomes, 10(2), p.13. https://doi.org/10.3390/proteomes10020013

141. Acharjee, A., Stephen Kingsly, J., Kamat, M., Kurlawala, V., Chakraborty, A., Vyas, P., Vaishnav, R. and Srivastava, S., 2022. Rise of the SARS-CoV-2 Variants: Can proteomics be the silver bullet?. Expert Review of Proteomics. https://doi.org/10.1080/14789450.2022.2085564

140. Mukherjee, A., Ghosh, S., Biswas, D., Rao, A., Shetty, P., Epari, S., Moiyadi, A. and Srivastava, S., 2022. Clinical Proteomics for Meningioma: An Integrated Workflow for Quantitative Proteomics and Biomarker Validation in Formalin-Fixed Paraffin-Embedded Tissue Samples. OMICS: A Journal of Integrative Biology, 26(9), pp.512-520. https://doi.org/10.1089/omi.2022.0082

139. Barpanda, A., Tuckley, C., Ray, A., Banerjee, A., Duttagupta, S.P., Kantharia, C. and Srivastava, S., 2022. A Protein Microarray‐Based Serum Proteomic Investigation Reveals Distinct Autoantibody Signature in Colorectal Cancer. PROTEOMICS–Clinical Applications, p.2200062. https://doi.org/10.1002/prca.202200062

138. Banerjee, A., Biswas, D., Barpanda, A., Halder, A., Sibal, S., Kattimani, R., Shah, A., Mahadevan, A., Goel, A. and Srivastava, S., 2022. The first Pituitary Proteome Landscape from matched anterior and posterior lobes for a better understanding of the Pituitary Gland. Molecular & Cellular Proteomics, p.100478 https://doi.org/10.1016/j.mcpro.2022.100478

137. Biswas, D., Kumari, N., Lachén-Montes, M., Dutta, S., Agrawal, I., Samanta, D., Shenoy, S.V., Halder, A., Fernández-Irigoyen, J., Padhye, A.R. and Santamaría, E., 2022. Deep Phosphoproteome Landscape of Interhemispheric Functionality of Neuroanatomical Regions of the Human Brain. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00244

136. Banerjee, A., Halder, A., Jadhav, P., Sarkar, A., Hole, A., Shastri, J.S., Agrawal, S., Chilakapati, M.K. and Srivastava, S., 2022. SARS‐CoV‐2 severity classification from plasma sample using confocal Raman spectroscopy. Journal of Raman Spectroscopy. https://doi.org/10.1002/jrs.6461

135. Banerjee, A., Ray, A., Barpanda, A., Dash, A., Gupta, I., Nissa, M. U., Zhu, H., Shah, A., Duttagupta, S. P., Goel, A., & Srivastava, S. (2022). Evaluation of autoantibody signatures in pituitary adenoma patients using human proteome arrays. PROTEOMICS – Clinical Applications, 16, e2100111. https://doi.org/10.1002/prca.202100111

134. Nissa, M.U., Reddy, P.J., Pinto, N., Sun, Z., Ghosh, B., Moritz, R.L., Goswami, M. and Srivastava, S., 2022. The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community. Scientific data, 9(1), pp.1-13. https://doi.org/10.1038/s41597-022-01259-9

133. Banerjee, A., Halder, A., Jadhav, P., Bankar, R., Pattarkine, J., Hole, A., Shah, A., Goel, A., Murali Krishna, C. and Srivastava, S., 2022. Metabolomics Profiling of Pituitary Adenomas by Raman Spectroscopy, Attenuated Total Reflection-Fourier Transform Infrared Spectroscopy, and Mass Spectrometry of Serum Samples. Analytical Chemistry, 94(34), pp.11898-11907. https://doi.org/10.1021/acs.analchem.2c02487 (Cover Page Article).

132. Ghosh, S., Parikh, S., Nissa, M.U., Acharjee, A., Singh, A., Patwa, D., Makwana, P., Athalye, A., Barpanda, A., Laloraya, M. and Srivastava, S., 2022. Semen Proteomics of COVID-19 Convalescent Men Reveals Disruption of Key Biological Pathways Relevant to Male Reproductive Function. ACS omega, 7(10), pp.8601-8612.https://doi.org/10.1021/acsomega.1c06551

131. Banerjee A., Pai MGJ, Singh A., UnNissa M., Srivastava S. “Mass spectrometry and proteome analysis to identify SARS-CoV-2 protein from COVID-19 patient swab samples” STAR Protocols. 2022. Volume 3, Issue 1, 18 March 2022, 101177 doi: https://doi.org/10.1016/j.xpro.2022.101177 .

130. Nissa MU, Pinto N, Mukherjee A, Reddy PJ, Ghosh B, Sun Z, Ghantasala S, Chetanya C, Shenoy SV, Moritz RL, Goswami M, Srivastava S. “Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita“ J Proteome Res. 2022. 21(2):420-437.https://doi.org/10.1021/acs.jproteome.1c00759 (Cover Page Article).

129. Shalini Aggarwal, Peng WK, Sanjeeva Srivastava. ” Multi-Omics Advancements towards Plasmodium vivax Malaria Diagnosis.” Diagnostics (Basel). 2021. 11(12):2222. doi: 10.3390/diagnostics11122222.

128. Deeptarup Biswas, Sanjyot Vinayak Shenoy, Chetanya Chetanya, Mercedes Lachén-Montes, Abhilash Barpanda, Arunachalam Paramasivan Athithyan, Susmita Ghosh, Karina Ausín, María Victoria Zelaya, Joaquín Fernández-Irigoyen, Akash Manna, Sudesh Roy, Arunasu Talukdar, Graham Roy Ball, Enrique Santamaría, Sanjeeva Srivastava. ” Deciphering the Interregional and Interhemisphere Proteome of the Human Brain in the Context of the Human Proteome Project” J Proteome Res. 2021. doi: 10.1021/acs.jproteome.1c00511. (Cover Page Article).

127. Manuel Fuentes, Sanjeeva Srivastava, Gronenborn AM, Joshua LaBaer. ” A Quantitative Systems Approach to Define Novel Effects of Tumour p53 Mutations on Binding Oncoprotein MDM2.” Int J Mol Sci. 2021. 23(1):53. doi: 10.3390/ijms23010053.

126. Ayushi Varma, Vipin Kumar, Saicharan Ghantasala, Sanjeeva Srivastava. “Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples” J Vis Exp. 2021 Nov 13;(177). doi: 10.3791/61786.

125. Amol Prakash, Lorne Taylor, Manu Varkey, Nate Hoxie, Yassene Mohammed, Young Ah Goo, Scott Peterman, Abhay Moghekar, Yuting Yuan, Trevor Glaros, Joel R Steele, Pouya Faridi, Shashwati Parihari, Sanjeeva Srivastava, Joseph J Otto, Julius O Nyalwidhe, O John Semmes, Michael F Moran, Anil Madugundu, Dong Gi Mun, Akhilesh Pandey, Keira E Mahoney, Jeffrey Shabanowitz, Satya Saxena, Benjamin C Orsburn “Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants” Cancers (Basel). 2021. 13(20):5034. doi: 10.3390/cancers13205034.

124. Rui Vitorino, Manisha Choudhury, Sofia Guedes, Rita Ferreira, Visith Thongboonkerd, Lakshya Sharma, Francisco Amado, Sanjeeva Srivastava. ” Peptidomics and proteogenomics: background, challenges and future needs” Expert Rev Proteomics. 2021. 18(8):643-659. doi: 10.1080/14789450.2021.1980388.

123. Saicharan Ghantasala, Medha Gayathri J Pai, Sanjeeva Srivastava. “Quantitative Proteomics Workflow using Multiple Reaction Monitoring Based Detection of Proteins from Human Brain Tissue” J Vis Exp. 2021. Aug 28;(174). doi: 10.3791/61833.

122. Karthikaichamy, A., Beardall, J., Coppel, R., Noronha, S., Bulach, D., Schittenhelm, R. B., & Srivastava, S. (2021). Data-Independent-Acquisition-Based Proteomic Approach towards Understanding the Acclimation Strategy of Oleaginous Microalga Microchloropsis gaditana CCMP526 in Hypersaline Conditions. ACS omega, 6(34), 22151–22164. https://doi.org/10.1021/acsomega.1c02786 (O)

121. Arghya Banerjee, Atul Goel, Abhidha Shah, Sanjeeva Srivastava “Recent advances in proteomics and its implications in pituitary endocrine disorders” Biochim Biophys Acta Proteins Proteom. 2021. 1869(11):140700. doi: 10.1016/j.bbapap.2021.140700.

120. Halder, Ankit, Ayushi Verma, Deeptarup Biswas, and Sanjeeva Srivastava. “Recent Advances in Mass-Spectrometry Based Proteomics Software, Tools and Databases.” Drug Discovery Today: Technologies, July 14, 2021. https://doi.org/10.1016/j.ddtec.2021.06.007. (T)

119. Amrita Mukherjee, Ayushi Verma, Surbhi Bihani, Ananya Burli, Krishi Mantri, Sanjeeva Srivastava. “Proteomics advances towards developing SARS-CoV-2 therapeutics using in silico drug repurposing approaches” Drug Discovery Today: Technologies. 2021 Dec;39:1-12. doi: 10.1016/j.ddtec.2021.06. 004.

118. Nissa, M.U., Pinto, N., Parkar, H., Goswami, M. and Srivastava, S., 2021. Proteomics in fisheries and aquaculture: An approach for food security. Food Control, P.108125. (O)

117. Suvarna K, Salkar A, Palanivel V, Bankar R, Banerjee N, Gayathri J Pai M, Srivastava A, Singh A, Khatri H, Agrawal S, Shrivastav O, Shastri J, Srivastava S. A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients. J Proteome Res. 2021 Aug 11:acs.jproteome.1c00215. doi: 10.1021/acs.jproteome.1c00215. Epub ahead of print. PMID: 34379420; PMCID: PMC8370121 (I)

116. Aggarwal, Shalini; Parihari, Shaswati; Banerjee, Arghya; Roy, Jyotirmoy; Baneerjee, Nirjhar; Choudhury, Manisha; Bankar, Renuka; Palanivel, Viswanthram; Salkar, Akanksha; Agrawal, Sachee; Shastri, Jayanthi; Srivastava, Sanjeeva*. “Metabolome and exposome profiling of the biospecimen from COVID-19 patients in India” Journal of Microbiology, Epidemiology and Immunobiology. (Accepted) (I)

115. Banerjee A, Gokhale A, Bankar R, Palanivel V, Salkar A, Robinson H, Shastri JS, Agrawal S, Hartel G, Hill MM, Srivastava S. Rapid Classification of COVID-19 Severity by ATR-FTIR Spectroscopy of Plasma Samples. Analytical Chemistry. 2021 Aug 3;93(30):10391-10396. doi: 10.1021/acs.analchem.1c00596. Epub 2021 Jul 19. PMID: 34279898; PMCID: PMC8315140. (I)

114. Mukherjee S, Biswas D, Epari S, Shetty P, Moiyadi A, Ball GR, Srivastava S*. Comprehensive proteomic analysis reveals distinct functional modules associated with skull base and supratentorial meningiomas and perturbations in collagen pathway components. J Proteomics. 2021 Jun 23:104303. doi: 10.1016/j.jprot.2021.104303. (C)

113. Barderas R, Srivastava S, LaBaer J*. Protein Microarray-Based Proteomics for Disease Analysis. Methods Mol Biol. 2021; 2344:3-6. doi: 10.1007/978-1-0716-1562-1_1. (B)

112. Gupta S, Banerjee A, Syed P, Srivastava S*. Profiling Autoantibody Responses to Devise Novel Diagnostic and Prognostic Markers Using High-Density Protein Microarrays. Methods Mol Biol. 2021; 2344:191-208. https://doi.org/10.1007/978-1-0716-1562-1_14 (B)

111. Venkatesh A, Jain A, Davies H, Felgner PL, Rathod PK, Patankar S, Srivastava S*. Protein Arrays for the Identification of Seroreactive Protein Markers for Infectious Diseases. Methods Mol Biol. 2021; 2344:139-150. https://doi.org/10.1007/978-1-0716-1562-1_10 (B)

110. Ghantasala S, Pai MGJ, Biswas D, Gahoi N, Mukherjee S, Kp M, Nissa MU, Srivastava A, Epari S, Shetty P, Moiyadi A, Srivastava S*. Multiple Reaction Monitoring-Based Targeted Assays for the Validation of Protein Biomarkers in Brain Tumors. Front Oncol. 2021 May 14; 11:548243. https://doi.org/10.3389/fonc.2021.548243 (C)

109. Thomas S, Kumar R, Sharma K, Barpanda A, Sreelakshmi Y, Sharma R, Srivastava S*. iTRAQ-based proteome profiling revealed the role of Phytochrome A in regulating primary metabolism in tomato seedling. Sci Rep 11, 7540 (2021). https://doi.org/10.1038/s41598-021-87208-9 (O)

108. Yadav R, Acharjee A, Salkar A, Bankar R, Palanivel V, Agrawal S, Shastri J, Sabnis SV, Srivastava S*. 2021. “Mumbai mayhem of COVID-19 pandemic reveals important factors that influence susceptibility to infection.” EClinical Medicine published by The Lancet. https://doi.org/10.1016/j.eclinm.2021.100841 (O)

107. Suvarna K, Biswas D, Pai MGJ, Acharjee A, Bankar R, Palanivel V, Salkar A, Verma A, Mukherjee A, Choudhury M, Ghantasala S, Ghosh S, Singh A, Banerjee A, Badaya A, Bihani S, Loya G, Mantri K, Burli A, Roy J, Srivastava A, Agrawal S, Shrivastav O, Shastri J, Srivastava S*. 2021. “Proteomics and Machine Learning Approaches Reveal a Set of Prognostic Markers for COVID-19 Severity with Drug Re-Purposing Potential.” Frontiers in Physiology. https://doi.org/10.3389/fphys.2021.652799 (I)

106. Bankar, R., Suvarna, K., Ghantasala, S., Banerjee, A., Biswas, D., Choudhury, M., Palanivel, V., Salkar, A., Verma, A., Singh, A., Mukherjee, A., Pai, M. G. J., Roy, J., Srivastava, A., Badaya, A., Agrawal, S., Shrivastav, O., Shastri, J., & Srivastava, S*. (2021). Proteomic investigation reveals dominant alterations of neutrophil degranulation and mRNA translation pathways in patients with COVID-19. IScience, 24(3), 102135. https://doi.org/10.1016/j.isci.2021.102135 (I)

105. Kp, M., Kumar, A., Biswas, D., Moiyadi, A., Shetty, P., Gupta, T., Epari, S., Shirsat, N., & Srivastava, S*. (2021). The proteomic analysis shows enrichment of RNA surveillance pathways in adult SHH and extensive metabolic reprogramming in Group 3 medulloblastomas. Brain Tumor Pathology. https://doi.org/10.1007/s10014-020-00391-x (C)

104. Aggarwal, S., Acharjee, A., Mukherjee, A., Baker, M. S., & Srivastava, S*. (2021). Role of Multiomics Data to Understand Host-Pathogen Interactions in COVID-19 Pathogenesis. Journal of Proteome Research, 20(2), 1107–1132. https://doi.org/10.1021/acs.jproteome.0c00771 (R)

103. Marathe, S., Dhamija, B., Kumar, S., Jain, N., Ghosh, S., Prakash, J., Srinivasan, S., Das, S., Sawant, A., Desai, S., Khan, F., Syiemlieh, A., Munde, M., Nayak, C., Gandhi, M., Kumar, A., Srivastava, S., Venkatesh, K. V., Barthel, S. R., & Purwar, R*. (2021). Multi-omics analysis and systems biology integration identifies the roles of IL-9 in keratinocyte metabolic reprogramming. The Journal of Investigative Dermatology. https://doi.org/10.1016/j.jid.2021.02.013 (O)

102. Kumar, V., Ray, S., Aggarwal, S., Biswas, D., Jadhav, M., Yadav, R., Sabnis, S. V., Banerjee, S., Talukdar, A., Kochar, S. K., Shetty, S., Sehgal, K., Patankar, S., & Srivastava, S*. (2020). Multiplexed quantitative proteomics provides mechanistic cues for malaria severity and complexity. Communications Biology, 3(1), 683.https://doi.org/10.1038/s42003-020-01384-4 (I)

101. Venkatesh, A., Aggarwal, S., Kumar, S., Rajyaguru, S., Kumar, V., Bankar, S., Shastri, J., Patankar, S., & Srivastava, S*. (2020). Comprehensive proteomics investigation of P. vivax-infected human plasma and parasite isolates. BMC Infectious Diseases, 20(1), 188. https://doi.org/10.1186/s12879-020-4885-3 (I)

100. Gahoi, N., Syed, P., Choudhary, S., Epari, S., Moiyadi, A., Varma, S. G., Gandhi, M. N., & Srivastava, S*. (2020). A Protein Microarray-Based Investigation of Cerebrospinal Fluid Reveals Distinct Autoantibody Signature in Low and High-Grade Gliomas. Frontiers in Oncology, 10, 543947. https://doi.org/10.3389/fonc.2020.543947 (C)

99. Kumar, V., Ray, S., Ghantasala, S., & Srivastava, S*. (2020). An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma. Frontiers in Oncology, 10, 543997. https://doi.org/10.3389/fonc.2020.543997 (C)

98. Mukherjee, S., Biswas, D., Gadre, R., Jain, P., Syed, N., Stylianou, J., Zeng, Q., Mahadevan, A., Epari, S., Shetty, P., Moiyadi, A., Roy Ball, G., & Srivastava, S*. (2020). Comprehending Meningioma Signaling Cascades Using Multipronged Proteomics Approaches & Targeted Validation of Potential Markers. Frontiers in Oncology, 10, 1600. https://doi.org/10.3389/fonc.2020.01600 (C)

97. Moiyadi, A., Shetty, P., Sridhar, E., Gota, V., Gurjar, M., Saicharan, G., Singh, V., & Srivastava, S*. (2020). Objective assessment of intraoperative tumor fluorescence reveals biological heterogeneity within glioblastomas: A biometric study. Journal of Neuro-Oncology, 146(3), 477–488. https://doi.org/10.1007/s11060-019-03338-1 (C)

96. Phapale, P., Rai, V., Mohanty, A. K., & Srivastava, S*. (2020). Untargeted Metabolomics Workshop Report: Quality Control Considerations from Sample Preparation to Data Analysis. Journal of the American Society for Mass Spectrometry, 31(9), 2006–2010. https://doi.org/10.1021/jasms.0c00224 (T)

95. Ray, S., & Srivastava, S*. (2020). COVID-19 Pandemic: Hopes from Proteomics and Multiomics Research. Omics: A Journal of Integrative Biology, 24(8), 457–459. https://doi.org/10.1089/omi.2020.0073 (R)

94. Verma, A., Halder, A., Marathe, S., Purwar, R., & Srivastava, S*. (2020). A proteogenomic approach to target neoantigens in solid tumors. Expert Review of Proteomics, 17(11–12), 797–812. https://doi.org/10.1080/14789450.2020.1881889 (R)

93. Ray, S., & Srivastava, S*. (2020). Virtualization of science education: A lesson from the COVID-19 pandemic. Journal of Proteins and Proteomics, 1–4. https://doi.org/10.1007/s42485-020-00038-7 (R)

92. Ghantasala, S., Gollapalli, K., Epari, S., Moiyadi, A., & Srivastava, S*. (2020). Glioma tumor proteomics: Clinically useful protein biomarkers and future perspectives. Expert Review of Proteomics, 17(3), 221–232. https://doi.org/10.1080/14789450.2020.1731310 (R)

91. Kakar-Bhanot, R., Brahmbhatt, K., Kumar, V., Suryawanshi, A. R., Srivastava, S., Chaudhari, U., & Sachdeva, G*. (2020). Plasma membrane proteome of adhesion-competent endometrial epithelial cells and its modulation by Rab11a. Molecular Reproduction and Development, 87(1), 17–29. https://doi.org/10.1002/mrd.23292 (O)

90. Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y.-K., Overall, C. M., Corrales, F. J., Cristea, I. M., Van Eyk, J. E., Uhlén, M., Lindskog, C., Chan, D. W., Bairoch, A., Waddington, J. C., Justice, J. L., LaBaer, J., Rodriguez, H., … Baker, M. S. (2020). A high-stringency blueprint of the human proteome. Nature Communications, 11(1), 5301. https://doi.org/10.1038/s41467-020-19045-9 (O)

89. Patel, S. K., Rajora, N., Kumar, S., Sahu, A., Kochar, S. K., Krishna, C. M., & Srivastava, S*. (2019). Rapid Discrimination of Malaria- and Dengue-Infected Patients Sera Using Raman Spectroscopy. Analytical Chemistry, 91(11), 7054–7062. https://doi.org/10.1021/acs.analchem.8b05907 (I)

88. Venkatesh, A., Jain, A., Davies, H., Periera, L., Maki, J. N., Gomes, E., Felgner, P. L., Srivastava, S*., Patankar, S., & Rathod, P. K. (2019). Hospital-derived antibody profiles of malaria patients in Southwest India. Malaria Journal, 18(1), 138. https://doi.org/10.1186/s12936-019-2771-5 (I)

87. Rao, A. A., Mehta, K., Gahoi, N., & Srivastava, S. (2019). Application of 2D-DIGE and iTRAQ Workflows to Analyze CSF in Gliomas. Methods in Molecular Biology (Clifton, N.J.), 2044, 81–110. https://doi.org/10.1007/978-1-4939-9706-0_6 (C)

86. Kakar-Bhanot R, Brahmbhatt K, Kumar V, Suryawanshi AR, Srivastava S, Chaudhari U, Sachdeva G*. Plasma membrane proteome of adhesion-competent endometrial epithelial cells and its modulation by Rab11a. Mol Reprod Dev. 2019 PMID: 31737970 https://doi.org/10.1002/mrd.23292 (O)

85. Mehta, K., Jaiswal, D., Nayak, M., Prasannan, C. B., Wangikar, P. P., & Srivastava, S*. (2019). Elevated carbon dioxide levels lead to proteome-wide alterations for optimal growth of a fast-growing cyanobacterium, Synechococcus elongatus PCC 11801. Scientific Reports, 9(1), 6257. https://doi.org/10.1038/s41598-019-42576-1 (O)

84. Awasthi, G., Tyagi, S., Kumar, V., Patel, S. K., Rojh, D., Sakrappanavar, V., Kochar, S. K., Talukdar, A., Samanta, B., Das, A., Srivastava, S., & Patankar, S*. (2018). A Proteogenomic Analysis of Haptoglobin in Malaria. Proteomics. Clinical Applications, 12(4), e1700077. https://doi.org/10.1002/prca.201700077 (I)

83. Venkatesh, A., Gil, C., Fuentes, M., LaBaer, J., & Srivastava, S*. (2018). A Perspective on Proteomics of Infectious Diseases. Proteomics. Clinical Applications, 12(4), e1700139. https://doi.org/10.1002/prca.201700139 (I)

82. Venkatesh, A., Lahiri, A., Reddy, P. J., Shastri, J., Bankar, S., Patankar, S., & Srivastava, S*. (2018). Identification of Highly Expressed Plasmodium Vivax Proteins from Clinical Isolates Using Proteomics. Proteomics. Clinical Applications, 12(4), e1700046. https://doi.org/10.1002/prca.201700046 (I)

81. Gahoi, N., Malhotra, D., Moiyadi, A., Varma, S. G., Gandhi, M. N., & Srivastava, S*. (2018). Multi-pronged proteomic analysis to study the glioma pathobiology using cerebrospinal fluid samples. Proteomics. Clinical Applications, 12(3), e1700056. https://doi.org/10.1002/prca.201700056 (C)

80. Mehta, K., Atak, A., Sahu, A., Srivastava, S., & C, M. K*. (2018). An early investigative serum Raman spectroscopy study of meningioma. The Analyst, 143(8), 1916–1923. https://doi.org/10.1039/c8an00224j (C)

79. Atak, A., Khurana, S., Gollapalli, K., Reddy, P. J., Levy, R., Ben-Salmon, S., Hollander, D., Donyo, M., Heit, A., Hotz-Wagenblatt, A., Biran, H., Sharan, R., Rane, S., Shelar, A., Ast, G., & Srivastava, S*. (2018). Quantitative mass spectrometry analysis reveals a panel of nine proteins as diagnostic markers for colon adenocarcinomas. Oncotarget, 9(17), 13530–13544. https://doi.org/10.18632/oncotarget.24418 (C)

78. Gahoi, N., Malhotra, D., Moiyadi, A., Varma, S. G., Gandhi, M. N., & Srivastava, S*. (2018). Multi-Pronged Proteomic Analysis to Study the Glioma Pathobiology using Cerebrospinal Fluid Samples. Proteomics. Clinical Applications, 12(2). https://doi.org/10.1002/prca.201870013 (C)

77. Srivastava, S. (2018). Proteomics-Based Investigations of Neglected and Tropical Diseases. Proteomics. Clinical Applications, 12(4), e1800076. https://doi.org/10.1002/prca.201800076 (R)

76. Karthikaichamy, A., Deore, P., Srivastava, S., Coppel, R., Bulach, D., Beardall, J., & Noronha, S*. (2018). Temporal acclimation of Microchloropsis gaditana CCMP526 in response to hypersalinity. Bioresource Technology, 254, 23–30. https://doi.org/10.1016/j.biortech.2018.01.062 (O)

75. Ray, S., Patel, S. K., Venkatesh, A., Chatterjee, G., Ansari, N. N., Gogtay, N. J., Thatte, U. M., Gandhe, P., Varma, S. G., Patankar, S., & Srivastava, S*. (2017). Quantitative Proteomics Analysis of Plasmodium vivax Induced Alterations in Human Serum during the Acute and Convalescent Phases of Infection. Scientific Reports, 7(1), 4400. https://doi.org/10.1038/s41598-017-04447-5 (I)

74. Gollapalli, K., Ghantasala, S., Kumar, S., Srivastava, R., Rapole, S., Moiyadi, A., Epari, S., & Srivastava, S*. (2017). Subventricular zone involvement in Glioblastoma—A proteomic evaluation and clinicoradiological correlation. Scientific Reports, 7(1), 1449. https://doi.org/10.1038/s41598-017-01202-8 (C)

73. Gollapalli, K., Ghantasala, S., Atak, A., Rapole, S., Moiyadi, A., Epari, S., & Srivastava, S*. (2017). Tissue Proteome Analysis of Different Grades of Human Gliomas Provides Major Cues for Glioma Pathogenesis. Omics: A Journal of Integrative Biology, 21(5), 275–284. https://doi.org/10.1089/omi.2017.0028 (C)

72. Gupta, S., Mukherjee, S., Syed, P., Pandala, N. G., Choudhary, S., Singh, V. A., Singh, N., Zhu, H., Epari, S., Noronha, S. B., Moiyadi, A., & Srivastava, S*. (2017). Evaluation of autoantibody signatures in meningioma patients using human proteome arrays. Oncotarget, 8(35), 58443–58456. https://doi.org/10.18632/oncotarget.16997 (C)

71. Jain, R., Atak, A., Yeola, A., & Srivastava, S*. (2017). Proteomic level changes associated with S3I201 treated U87 glioma cells. Journal of Proteomics, 150, 341–350. https://doi.org/10.1016/j.jprot.2016.08.011 (C)

70. Jadhav, M., Nayak, M., Kumar, S., Venkatesh, A., Patel, S. K., Kumar, V., Sharma, S., Samanta, B., Deb, S., Karak, A., Verma, S., Talukdar, A., Kochar, S. K., Mansukhani, P., Gandhi, M., & Srivastava, S*. (2017). Clinical Proteomics and Cytokine Profiling for Dengue Fever Disease Severity Biomarkers. Omics: A Journal of Integrative Biology, 21(11), 665–677. https://doi.org/10.1089/omi.2017.0135 (R)

69. Özdemir, V., Dove, E. S., Gürsoy, U. K., Şardaş, S., Yıldırım, A., Yılmaz, Ş. G., Ömer Barlas, I., Güngör, K., Mete, A., & Srivastava, S*. (2017). Personalized medicine beyond genomics: Alternative futures in big data-proteomics, environtome and the social proteome. Journal of Neural Transmission (Vienna, Austria: 1996), 124(1), 25–32. https://doi.org/10.1007/s00702-015-1489-y (R)

68. Karthikaichamy, A., Deore, P., Rai, V., Bulach, D., Beardall, J., Noronha, S., & Srivastava, S*. (2017). Time for Multiple Extraction Methods in Proteomics? A Comparison of Three Protein Extraction Methods in the Eustigmatophyte Alga Microchloropsis gaditana CCMP526. Omics: A Journal of Integrative Biology, 21(11), 678–683. https://doi.org/10.1089/omi.2017.0128 (O)

67. Rai, V., Muthuraj, M., Gandhi, M. N., Das, D., & Srivastava, S*. (2017). Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae. Scientific Reports, 7, 45732. https://doi.org/10.1038/srep45732 (O)

66. Gupta, S., Manubhai, K. P., Mukherjee, S., & Srivastava, S*. (2017). Serum Profiling for Identification of Autoantibody Signatures in Diseases Using Protein Microarrays. Methods in Molecular Biology (Clifton, N.J.), 1619, 303–315.https://doi.org/10.1007/978-1-4939-7057-5_21 (O)

65. Ray, S., Patel, S. K., Venkatesh, A., Bhave, A., Kumar, V., Singh, V., Chatterjee, G., Shah, V. G., Sharma, S., Renu, D., Nafis, N., Gandhe, P., Gogtay, N., Thatte, U., Sehgal, K., Verma, S., Karak, A., Khanra, D., Talukdar, A., … Srivastava, S*. (2016). Clinicopathological Analysis and Multipronged Quantitative Proteomics Reveal Oxidative Stress and Cytoskeletal Proteins as Possible Markers for Severe Vivax Malaria. Scientific Reports, 6, 24557. https://doi.org/10.1038/srep24557 (I)

64. Paul, D., Chanukuppa, V., Reddy, P. J., Taunk, K., Adhav, R., Srivastava, S., Santra, M. K., & Rapole, S*. (2016). Global proteomic profiling identifies etoposide chemoresistance markers in non-small cell lung carcinoma. Journal of Proteomics, 138, 95–105. https://doi.org/10.1016/j.jprot.2016.02.008 (C)

63. Srivastava, S. (2016). Protein arrays: Promises and potential for the translational research. Proteomics, 16(8), 1191–1192. https://doi.org/10.1002/pmic.201600131 (R)

62. Atak, A., Mukherjee, S., Jain, R., Gupta, S., Singh, V. A., Gahoi, N., K P, M., & Srivastava, S*. (2016). Protein microarray applications: Autoantibody detection and posttranslational modification. Proteomics, 16(19), 2557–2569. https://doi.org/10.1002/pmic.201600104 (O)

61. Kumar, R., & Srivastava, S. (2016). Quantitative proteomic comparison of stationary/G0 phase cells and tetrads in budding yeast. Scientific Reports, 6, 32031. https://doi.org/10.1038/srep32031 (O)

60. Rai, V., Karthikaichamy, A., Das, D., Noronha, S., Wangikar, P. P., & Srivastava, S*. (2016). Multi-omics Frontiers in Algal Research: Techniques and Progress to Explore Biofuels in the Postgenomics World. Omics: A Journal of Integrative Biology, 20(7), 387–399. https://doi.org/10.1089/omi.2016.0065 (O)

59. Atak, A., Mehta, K., Rao, A., Gollapalli, K., Manubhai, K. P., Gandhi, M., Nayak, M., Gahoi, N., Reddy, P. J., Jain, R., Ghantasala, S., Gupta, S., Mukherjee, S., Pillai, T., Singh, V. A., Mani, V. A., Pandey, V., & Srivastava, S*. (2016). Targeted Proteomics Workshop and International Symposium (IIT Bombay, Mumbai, India): An Accelerator for Global Proteomics. Omics: A Journal of Integrative Biology, 20(4), 199–201. https://doi.org/10.1089/omi.2016.0037 (O)

58. Gupta, S., Manubhai, K. P., Kulkarni, V., & Srivastava, S*. (2016). An overview of innovations and industrial solutions in Protein Microarray Technology. Proteomics, 16(8), 1297–1308. https://doi.org/10.1002/pmic.201500429 (O)

57. Saygılı, E. İ., Abou-Zeid, A. H., Akkın, S. M., Aklillu, E., Barlas, İ. Ö., Borda-Rodriguez, A., Boschele, F. A., Çetin, Z., Coşkun, E., Coşkun, Y., Dağlı, G., Dai, T. U., Dandara, C., Dereli, T., Elbeyli, L., Endrenyi, L., Eyigün, C. P., Georgakilas, A., Günbulut, B., … Hekim, N*. (2016). An Open Letter in Support of Transformative Biotechnology and Social Innovation: SANKO University Innovation Summit in Medicine and Integrative Biology, Gaziantep, Turkey, May 5-7, 2016. Omics: A Journal of Integrative Biology, 20(4), 259–262. https://doi.org/10.1089/omi.2016.0038 (O)

56. Ray, S., Kumar, V., Bhave, A., Singh, V., Gogtay, N. J., Thatte, U. M., Talukdar, A., Kochar, S. K., Patankar, S., & Srivastava, S*. (2015). Proteomic analysis of Plasmodium falciparum induced alterations in humans from different endemic regions of India to decipher malaria pathogenesis and identify surrogate markers of severity. Journal of Proteomics, 127(Pt A), 103–113. https://doi.org/10.1016/j.jprot.2015.04.032 (I)

55. Sahu, A. K., Dhoot, S., Singh, A., Sawant, S. S., Nandakumar, N., Talathi-Desai, S., Garud, M., Pagare, S., Srivastava, S., Nair, S., Chaturvedi, P., & Murali Krishna, C*. (2015). Oral cancer screening: Serum Raman spectroscopic approach. Journal of Biomedical Optics, 20(11), 115006. https://doi.org/10.1117/1.JBO.20.11.115006 (C)

54. Syed, P., Gupta, S., Choudhary, S., Pandala, N. G., Atak, A., Richharia, A., K P, M., Zhu, H., Epari, S., Noronha, S. B., Moiyadi, A., & Srivastava, S*. (2015). Autoantibody Profiling of Glioma Serum Samples to Identify Biomarkers Using Human Proteome Arrays. Scientific Reports, 5, 13895. https://doi.org/10.1038/srep13895 (C)

53. Sharma, S., Ray, S., Mukherjee, S., Moiyadi, A., Sridhar, E., & Srivastava, S*. (2015). Multipronged quantitative proteomic analyses indicate modulation of various signal transduction pathways in human meningiomas. Proteomics, 15(2–3), 394–407. https://doi.org/10.1002/pmic.201400328 (C)

52. Reddy, P. J., Ray, S., & Srivastava, S*. (2015). The quest of the human proteome and the missing proteins: Digging deeper. Omics: A Journal of Integrative Biology, 19(5), 276–282. https://doi.org/10.1089/omi.2015.0035 (R)

51. Gahoi, N., Ray, S., & Srivastava, S*. (2015). Array-based proteomic approaches to study signal transduction pathways: Prospects, merits and challenges. Proteomics, 15(2–3), 218–231. https://doi.org/10.1002/pmic.201400261 (R)

50. Grover Shah, V., Ray, S., Karlsson, R., & Srivastava, S*. (2015). Calibration-free concentration analysis of protein biomarkers in human serum using surface plasmon resonance. Talanta, 144, 801–808. https://doi.org/10.1016/j.talanta.2015.06.074 (O)

49. Reddy, P. J., Atak, A., Ghantasala, S., Kumar, S., Gupta, S., Prasad, T. S. K., Zingde, S. M., & Srivastava, S*. (2015). Proteomics research in India: An update. Journal of Proteomics, 127(Pt A), 7–17. https://doi.org/10.1016/j.jprot.2015.04.002(O)

48. Srivastava, S*. (2015). Special Issue “Proteomics in India”: Gazing Forward while Reflecting on the Lessons Learned in Global Proteomics. Journal of Proteomics, 127(Pt A), 1–2. https://doi.org/10.1016/j.jprot.2015.09.017 (O)

47. Dove, E. S., Barlas, I. Ö., Birch, K., Boehme, C., Borda-Rodriguez, A., Byne, W. M., Chaverneff, F., Coşkun, Y., Dahl, M.-L., Dereli, T., Diwakar, S., Elbeyli, L., Endrenyi, L., Eroğlu-Kesim, B., Ferguson, L. R., Güngör, K., Gürsoy, U., Hekim, N., Huzair, F., … Özdemir, V*. (2015). An Appeal to the Global Health Community for a Tripartite Innovation: An “Essential Diagnostics List,” “Health in All Policies,” and “See-Through 21st Century Science and Ethics.” Omics: A Journal of Integrative Biology, 19(8), 435–442. https://doi.org/10.1089/omi.2015.0075 (O)

46. Gupta, S., Reddy, P. J., Ray, S., Atak, A., Gollapalli, K., Jain, R., Shah, V. G., Ghantasala, S., Kumar, S., Pandala, N. G., Phapale, P., Pandey, V. K., Zingde, S., & Srivastava, S*. (2015). Meeting Report: “Proteomics from Discovery to Function:” 6th Annual Meeting of Proteomics Society, India and International Conference-A Milestone for the Indian Proteomics Community. Omics: A Journal of Integrative Biology, 19(6), 329–331. https://doi.org/10.1089/omi.2015.0044 (O)

45. Özdemir, V., Faris, J., & Srivastava, S*. (2015). Crowdfunding 2.0: The next-generation philanthropy: a new approach for philanthropists and citizens to co-fund disruptive innovation in global health. EMBO Reports, 16(3), 267–271. https://doi.org/10.15252/embr.201439548 (O)

44. Reddy, P. J., Ray, S., Sathe, G. J., Gajbhiye, A., Prasad, T. S. K., Rapole, S., Panda, D., & Srivastava, S*. (2015). A comprehensive proteomic analysis of totarol induced alterations in Bacillus subtilis by multipronged quantitative proteomics. Journal of Proteomics, 114, 247–262. https://doi.org/10.1016/j.jprot.2014.10.025 (O)

43. Jain, R., Kulkarni, P., Dhali, S., Rapole, S., & Srivastava, S*. (2015). Quantitative proteomic analysis of global effect of LLL12 on U87 cell’s proteome: An insight into the molecular mechanism of LLL12. Journal of Proteomics, 113, 127–142. https://doi.org/10.1016/j.jprot.2014.09.020 (O)

42. Reddy, P. J., Ray, S., Sathe, G. J., Prasad, T. S. K., Rapole, S., Panda, D., & Srivastava, S*. (2015). Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone. Omics: A Journal of Integrative Biology, 19(1), 12–23. https://doi.org/10.1089/omi.2014.0099 (O)

41. Reddy, P. J., Sinha, S., Ray, S., Sathe, G. J., Chatterjee, A., Prasad, T. S. K., Dhali, S., Srikanth, R., Panda, D., & Srivastava, S*. (2015). Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment. PloS One, 10(4), e0120620. https://doi.org/10.1371/journal.pone.0120620 (O)

40. Reddy, P. J., Sinha, S., Ray, S., Sathe, G. J., Chatterjee, A., Prasad, T. S. K., Dhali, S., Srikanth, R., Panda, D., & Srivastava, S*. (2015). Correction: Comprehensive Analysis of Temporal Alterations in Cellular Proteome of Bacillus subtilis under Curcumin Treatment. PloS One, 10(6), e0130782. https://doi.org/10.1371/journal.pone.0130782 (O)

39. Ray, S., Patel, S. K., Kumar, V., Damahe, J., & Srivastava, S*. (2014). Differential expression of serum/plasma proteins in various infectious diseases: Specific or nonspecific signatures. Proteomics. Clinical Applications, 8(1–2), 53–72. https://doi.org/10.1002/prca.201300074 (I)

38. Sharma, S., Ray, S., Moiyadi, A., Sridhar, E., & Srivastava, S*. (2014). Quantitative proteomic analysis of meningiomas for the identification of surrogate protein markers. Scientific Reports, 4, 7140. https://doi.org/10.1038/srep07140 (C)

37. Moiyadi, A., Syed, P., & Srivastava, S*. (2014). Fluorescence-guided surgery of malignant gliomas based on 5-aminolevulinic acid: Paradigm shifts but not a panacea. Nature Reviews. Cancer, 14(2), 146. https://doi.org/10.1038/nrc3566-c1 (C)

36. Gupta, S., Venkatesh, A., Ray, S., & Srivastava, S*. (2014). Challenges and prospects for biomarker research: A current perspective from the developing world. Biochimica Et Biophysica Acta, 1844(5), 899–908. https://doi.org/10.1016/j.bbapap.2013.12.020 (R)

35. Kumar, R., Dhali, S., Srikanth, R., Ghosh, S. K., & Srivastava, S*. (2014). Comparative proteomics of mitosis and meiosis in Saccharomyces cerevisiae. Journal of Proteomics, 109, 1–15. https://doi.org/10.1016/j.jprot.2014.06.006 (O)

34. Hekim, N., Coşkun, Y., Sınav, A., Abou-Zeid, A. H., Ağırbaşlı, M., Akintola, S. O., Aynacıoğlu, Ş., Bayram, M., Bragazzi, N. L., Dandara, C., Dereli, T., Dove, E. S., Elbeyli, L., Endrenyi, L., Erciyas, K., Faris, J., Ferguson, L. R., Göğüş, F., Güngör, K., … Özdemir, V*. (2014). Translating biotechnology to knowledge-based innovation, peace, and development? Deploy a Science Peace Corps–an open letter to world leaders. Omics: A Journal of Integrative Biology, 18(7), 415–420. https://doi.org/10.1089/omi.2014.0079 (O)

33. Ozdemir, V., Endrenyi, L., Aynacıoğlu, S., Bragazzi, N. L., Dandara, C., Dove, E. S., Ferguson, L. R., Geraci, C. J., Hafen, E., Kesim, B. E., Kolker, E., Lee, E. J. D., Llerena, A., Nacak, M., Shimoda, K., Someya, T., Srivastava, S., Tomlinson, B., Vayena, E., … Yaşar, U*. (2014). Bernard Lerer: Recipient of the 2014 inaugural Werner Kalow Responsible Innovation Prize in Global Omics and Personalized Medicine (Pacific Rim Association for Clinical Pharmacogenetics). Omics: A Journal of Integrative Biology, 18(4), 211–221. https://doi.org/10.1089/omi.2014.0029 (O)

32. Rao, A. A., Patkari, M., Reddy, P. J., Srivastava, R., Pendharkar, N., Rapole, S., Mehra, S., & Srivastava, S*. (2014). Proteomic analysis of Streptomyces coelicolor in response to Ciprofloxacin challenge. Journal of Proteomics, 97, 222–234. https://doi.org/10.1016/j.jprot.2013.08.013 (O)

31. Kolker, E., Özdemir, V., Martens, L., Hancock, W., Anderson, G., Anderson, N., Aynacioglu, S., Baranova, A., Campagna, S. R., Chen, R., Choiniere, J., Dearth, S. P., Feng, W.-C., Ferguson, L., Fox, G., Frishman, D., Grossman, R., Heath, A., Higdon, R., … Yandl, G*. (2014). Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. Omics: A Journal of Integrative Biology, 18(1), 10–14. https://doi.org/10.1089/omi.2013.0149 (O)

30. Özdemir, V., Kolker, E., Hotez, P. J., Mohin, S., Prainsack, B., Wynne, B., Vayena, E., Coşkun, Y., Dereli, T., Huzair, F., Borda-Rodriguez, A., Bragazzi, N. L., Faris, J., Ramesar, R., Wonkam, A., Dandara, C., Nair, B., Llerena, A., Kılıç, K., … Kickbusch, I*. (2014). Ready to put metadata on the post-2015 development agenda? Linking data publications to responsible innovation and science diplomacy. Omics: A Journal of Integrative Biology, 18(1), 1–9. https://doi.org/10.1089/omi.2013.0170 (O)

29. Diwakar, S., Parasuram, H., Medini, C., Raman, R., Nedungadi, P., Wiertelak, E., Srivastava, S., Achuthan, K., & Nair, B*. (2014). Complementing Neurophysiology Education for Developing Countries via Cost-Effective Virtual Labs: Case Studies and Classroom Scenarios. Journal of Undergraduate Neuroscience Education: JUNE: A Publication of FUN, Faculty for Undergraduate Neuroscience, 12(2), A130-139. (O)

28. Kolker, E., Özdemir, V., Martens, L., Hancock, W., Anderson, G., Anderson, N., Aynacioglu, S., Baranova, A., Campagna, S. R., Chen, R., Choiniere, J., Dearth, S. P., Feng, W.-C., Ferguson, L., Fox, G., Frishman, D., Grossman, R., Heath, A., Higdon, R., … Yandl, G*. (2013). Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. Big Data, 1(4), 196–201. https://doi.org/10.1089/big.2013.0039 (T)

27. Özdemir, V., Badr, K. F., Dove, E. S., Endrenyi, L., Geraci, C. J., Hotez, P. J., Milius, D., Neves-Pereira, M., Pang, T., Rotimi, C. N., Sabra, R., Sarkissian, C. N., Srivastava, S., Tims, H., Zgheib, N. K., & Kickbusch, I*. (2013). Crowd-funded micro-grants for genomics and “big data”: An actionable idea connecting small (artisan) science, infrastructure science, and citizen philanthropy. Omics: A Journal of Integrative Biology, 17(4), 161–172. https://doi.org/10.1089/omi.2013.0034 (T)

26. Ray, S., Moiyadi, A., & Srivastava, S*. (2013). Epidemiology: Biorepositories for cancer research in developing countries. Nature Reviews. Clinical Oncology, 10(8), 434–436. https://doi.org/10.1038/nrclinonc.2013.119 (R)

25. Konvalinka, A., Srivastava, S., & Masellis, M*. (2013). Taking the Kidney Personally: The Quest for Novel Antigens of Idiopathic Membranous Nephropathy through Proteomic Approaches – Per Ardua Ad Astra? Current Pharmacogenomics and Personalized Medicine, 11(1), 5–7. https://doi.org/10.2174/1875692111311010002 (R)

24. Srivastava, S., Özdemir, V., Ray, S., Panga, J. R., Noronha, S., Nair, B., & Diwakar, S*. (2013). Online education: E-learning booster in developing world. Nature, 501(7467), 316. https://doi.org/10.1038/501316c (O)

23. Mehta, G. D., Kumar, R., Srivastava, S., & Ghosh, S. K*. (2013). Cohesin: Functions beyond sister chromatid cohesion. FEBS Letters, 587(15), 2299–2312. https://doi.org/10.1016/j.febslet.2013.06.035 (O)

22. Kolker, E., Altintas, I., Bourne, P., Faris, J., Fox, G., Frishman, D., Geraci, C., Hancock, W., Lin, B., Lancet, D., Lisitsa, A., Knight, R., Martens, L., Mesirov, J., Özdemir, V., Schultes, E., Smith, T., Snyder, M., Srivastava, S., … Wilmes, P*. (2013). Reproducibility: In praise of open research measures. Nature, 498(7453), 170. https://doi.org/10.1038/498170b (O)

21. Ozdemir, V., Borda-Rodriguez, A., Dove, E. S., Ferguson, L. R., Huzair, F., Manolopoulos, V. G., Masellis, M., Milius, D., Warnich, L., & Srivastava, S*. (2013). Public Health Pharmacogenomics and the Design Principles for Global Public Goods—Moving Genomics to Responsible Innovation. Current Pharmacogenomics and Personalized Medicine, 11(1), 1–4. https://doi.org/10.2174/1875692111311010001 (O)

20. Srivastava, R., Ray, S., Vaibhav, V., Gollapalli, K., Jhaveri, T., Taur, S., Dhali, S., Gogtay, N., Thatte, U., Srikanth, R., & Srivastava, S*. (2012). Serum profiling of leptospirosis patients to investigate proteomic alterations. Journal of Proteomics, 76 Spec No., 56–68. https://doi.org/10.1016/j.jprot.2012.04.007 (I)

19. Ray, S., Srivastava, R., Tripathi, K., Vaibhav, V., Patankar, S., & Srivastava, S*. (2012). Serum proteome changes in dengue virus-infected patients from a dengue-endemic area of India: Towards new molecular targets? Omics: A Journal of Integrative Biology, 16(10), 527–536. https://doi.org/10.1089/omi.2012.0037 (I)

18. Gollapalli, K., Ray, S., Srivastava, R., Renu, D., Singh, P., Dhali, S., Bajpai Dikshit, J., Srikanth, R., Moiyadi, A., & Srivastava, S*. (2012). Investigation of serum proteome alterations in human glioblastoma multiforme. Proteomics, 12(14), 2378–2390. https://doi.org/10.1002/pmic.201200002 (C)

17. Ray, S., Kamath, K. S., Srivastava, R., Raghu, D., Gollapalli, K., Jain, R., Gupta, S. V., Ray, S., Taur, S., Dhali, S., Gogtay, N., Thatte, U., Srikanth, R., Patankar, S., & Srivastava, S*. (2012). Serum proteome analysis of vivax malaria: An insight into the disease pathogenesis and host immune response. Journal of Proteomics, 75(10), 3063–3080. https://doi.org/10.1016/j.jprot.2011.10.018 (I)

16. Mohammadi, M., Srivastava, S., Hall, J. C., Kav, N. N. V., & Deyholos, M. K.* (2012). Two wheat (Triticum aestivum) pathogenesis-related 10 (PR-10) transcripts with distinct patterns of abundance in different organs. Molecular Biotechnology, 51(2), 103–108. https://doi.org/10.1007/s12033-011-9441-3 (O)

15. Ray, S., Koshy, N. R., Reddy, P. J., & Srivastava, S*. (2012). Virtual Labs in proteomics: New E-learning tools. Journal of Proteomics, 75(9), 2515–2525. https://doi.org/10.1016/j.jprot.2012.03.014 (T)

14. Reddy, P. J., Sadhu, S., Ray, S., & Srivastava, S*. (2012). Cancer biomarker detection by surface plasmon resonance biosensors. Clinics in Laboratory Medicine, 32(1), 47–72. https://doi.org/10.1016/j.cll.2011.11.002 (C)

13. Ray, S., Koshy, N. R., Diwakar, S., Nair, B., & Srivastava, S*. (2012). Sakshat Labs: India’s virtual proteomics initiative. PLoS Biology, 10(7), e1001353. https://doi.org/10.1371/journal.pbio.1001353 (T)

12. Ray, S., Renu, D., Srivastava, R., Gollapalli, K., Taur, S., Jhaveri, T., Dhali, S., Chennareddy, S., Potla, A., Dikshit, J. B., Srikanth, R., Gogtay, N., Thatte, U., Patankar, S., & Srivastava, S*. (2012). Proteomic investigation of falciparum and vivax malaria for identification of surrogate protein markers. PloS One, 7(8), e41751. https://doi.org/10.1371/journal.pone.0041751 (I)

11. Kamath, K. S., Vasavada, M. S., & Srivastava, S*. (2011). Proteomic databases and tools to decipher post-translational modification. Journal of Proteomics, 75(1), 127–144. https://doi.org/10.1016/j.jprot.2011.09.014 (R)

10. Chandra, H., Reddy, P. J., & Srivastava, S. (2011). Protein microarrays and novel detection platforms. Expert Review of Proteomics, 8(1), 61–79. https://doi.org/10.1586/epr.10.99

9. Ray, S., Reddy, P. J., Choudhary, S., Raghu, D., & Srivastava, S*. (2011). Emerging nanoproteomics approaches for disease biomarker detection: A current perspective. Journal of Proteomics, 74(12), 2660–2681. https://doi.org/10.1016/j.jprot.2011.04.027

8. Ozdemir, V., Rosenblatt, D. S., Warnich, L., Srivastava, S., Tadmouri, G. O., Aziz, R. K., Reddy, P. J., Manamperi, A., Dove, E. S., Joly, Y., Zawati, M. H., Hızel, C., Yazan, Y., John, L., Vaast, E., Ptolemy, A. S., Faraj, S. A., Kolker, E., & Cotton, R. G. H*. (2011). Towards an Ecology of Collective Innovation: Human Variome Project (HVP), Rare Disease Consortium for Autosomal Loci (RaDiCAL) and Data-Enabled Life Sciences Alliance (DELSA). Current Pharmacogenomics and Personalized Medicine, 9(4), 243–251. https://doi.org/10.2174/187569211798377153

7. Kamal, S. M., Warnich, L., Ferguson, L. R., Srivastava, S., Ray, S., Avard, D., Joly, Y., Le Huynh, M., Page, M., Masellis, M., Dove, E. S., Gurwitz, D., & Ozdemir, V*. (2011). Forward Look: Tenth Anniversary of the Human Genome Sequence and 21 Century Postgenomics Global Health – A Close Up on Africa and Women’s Health. Current Pharmacogenomics and Personalized Medicine, 9(3), 148–155. https://doi.org/10.2174/187569211796957511

6. Ray, S., Reddy, P. J., Jain, R., Gollapalli, K., Moiyadi, A., & Srivastava, S*. (2011). Proteomic technologies for the identification of disease biomarkers in serum: Advances and challenges ahead. Proteomics, 11(11), 2139–2161. https://doi.org/10.1002/pmic.201000460

5. Reddy, P. J., Jain, R., Paik, Y.-K., Downey, R., Ptolemy, A. S., Ozdemir, V., & Srivastava, S*. (2011). Personalized Medicine in the Age of Pharmacoproteomics: A Close up on India and Need for Social Science Engagement for Responsible Innovation in Post-Proteomic Biology. Current Pharmacogenomics and Personalized Medicine, 9(1), 67–75. https://doi.org/10.2174/187569211794728850

4. Chatterji, B. P., Jindal, B., Srivastava, S., & Panda, D*. (2011). Microtubules as antifungal and antiparasitic drug targets. Expert Opinion on Therapeutic Patents, 21(2), 167–186. https://doi.org/10.1517/13543776.2011.545349

3. Ray, S., Chandra, H., & Srivastava, S*. (2010). Nano techniques in proteomics: Current status, promises and challenges. Biosensors & Bioelectronics, 25(11), 2389–2401. https://doi.org/10.1016/j.bios.2010.04.010 (R)

2. Chandra, H., & Srivastava, S*. (2010). Cell-free synthesis-based protein microarrays and their applications. Proteomics, 10(4), 717–730. https://doi.org/10.1002/pmic.200900462 (R)

1. Ray, S., Mehta, G., & Srivastava, S*. (2010). Label-free detection techniques for protein microarrays: Prospects, merits and challenges. Proteomics, 10(4), 731–748. https://doi.org/10.1002/pmic.200900458 (R)