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14 results on '"Dwivedi, Sutopa B."'

2. Annotation of the Zebrafish Genome through an Integrated Transcriptomic and Proteomic Analysis

Author

Kelkar, Dhanashree S, Provost, Elayne, Chaerkady, Raghothama, Muthusamy, Babylakshmi, Manda, Srikanth S, Subbannayya, Tejaswini, Selvan, Lakshmi Dhevi N, Wang, Chieh-Huei, Datta, Keshava K, Woo, Sunghee, Dwivedi, Sutopa B, Renuse, Santosh, Getnet, Derese, Huang, Tai-Chung, Kim, Min-Sik, Pinto, Sneha M, Mitchell, Christopher J, Madugundu, Anil K, Kumar, Praveen, Sharma, Jyoti, Advani, Jayshree, Dey, Gourav, Balakrishnan, Lavanya, Syed, Nazia, Nanjappa, Vishalakshi, Subbannayya, Yashwanth, Goel, Renu, Prasad, TS Keshava, Bafna, Vineet, Sirdeshmukh, Ravi, Gowda, Harsha, Wang, Charles, Leach, Steven D, and Pandey, Akhilesh

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Amino Acid Sequence, Animals, Base Sequence, Gene Expression Profiling, Genome, High-Throughput Nucleotide Sequencing, Mass Spectrometry, Molecular Sequence Annotation, Proteome, Proteomics, Sequence Analysis, RNA, Transcriptome, Zebrafish, Biochemistry & Molecular Biology
Abstract

Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and ∼ 69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes.

Published
2014

4. A comprehensive curated resource for follicle stimulating hormone signaling

Author

Sharma Jyoti, Raju Rajesh, Dwivedi Sutopa B, Palapetta Shyam, Ambekar Aditi, Telikicherla Deepthi, Prasad TS Keshava, Ramachandra YL, Mohan S Sujatha, Maharudraiah Jagadeesha, Mukherjee Srabani, and Pandey Akhilesh

Subjects
Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Background Follicle stimulating hormone (FSH) is an important hormone responsible for growth, maturation and function of the human reproductive system. FSH regulates the synthesis of steroid hormones such as estrogen and progesterone, proliferation and maturation of follicles in the ovary and spermatogenesis in the testes. FSH is a glycoprotein heterodimer that binds and acts through the FSH receptor, a G-protein coupled receptor. Although online pathway repositories provide information about G-protein coupled receptor mediated signal transduction, the signaling events initiated specifically by FSH are not cataloged in any public database in a detailed fashion. Findings We performed comprehensive curation of the published literature to identify the components of FSH signaling pathway and the molecular interactions that occur upon FSH receptor activation. Our effort yielded 64 reactions comprising 35 enzyme-substrate reactions, 11 molecular association events, 11 activation events and 7 protein translocation events that occur in response to FSH receptor activation. We also cataloged 265 genes, which were differentially expressed upon FSH stimulation in normal human reproductive tissues. Conclusions We anticipate that the information provided in this resource will provide better insights into the physiological role of FSH in reproductive biology, its signaling mediators and aid in further research in this area. The curated FSH pathway data is freely available through NetPath (http://www.netpath.org), a pathway resource developed previously by our group.

Published
2011
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5. Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

Author

Prasad, T. S. Keshava, Mohanty, Ajeet Kumar, Kumar, Manish, Sreenivasamurthy, Sreelakshmi K., Dey, Gourav, Nirujogi, Raja Sekhar, Pinto, Sneha M., Madugundu, Anil K., Pati, Arun H., Advani, Jayshree, Manda, Srikanth S., Gupta, Manoj Kumar, Dwivedi, Sutopa B., Kelkar, Dhanashree S., Hall, Brantley, Jiang, Xiaofang, Peery, Ashley, Rajagopalan, Pavithra, Yelamanchi, Soujanya D., Solanki, Hitendra S., Raja, Remya, Sathe, Gajanan J., Chavan, Sandip, Verma, Renu, Patel, Krishna M., Jain, Ankit P., Syed, Nazia, Datta, Keshava K., Khan, Aafaque Ahmed, Dammalli, Manjunath, Jayaram, Savita, Radhakrishnan, Aneesha, Mitchell, Christopher J., Na, Chan-Hyun, Kumar, Nirbhay, Sinnis, Photini, Sharakhov, Igor V., Wang, Charles, Gowda, Harsha, Tu, Zhijian Jake, Kumar, Ashwani, Pandey, Akhilesh, Prasad, T. S. Keshava, Mohanty, Ajeet Kumar, Kumar, Manish, Sreenivasamurthy, Sreelakshmi K., Dey, Gourav, Nirujogi, Raja Sekhar, Pinto, Sneha M., Madugundu, Anil K., Pati, Arun H., Advani, Jayshree, Manda, Srikanth S., Gupta, Manoj Kumar, Dwivedi, Sutopa B., Kelkar, Dhanashree S., Hall, Brantley, Jiang, Xiaofang, Peery, Ashley, Rajagopalan, Pavithra, Yelamanchi, Soujanya D., Solanki, Hitendra S., Raja, Remya, Sathe, Gajanan J., Chavan, Sandip, Verma, Renu, Patel, Krishna M., Jain, Ankit P., Syed, Nazia, Datta, Keshava K., Khan, Aafaque Ahmed, Dammalli, Manjunath, Jayaram, Savita, Radhakrishnan, Aneesha, Mitchell, Christopher J., Na, Chan-Hyun, Kumar, Nirbhay, Sinnis, Photini, Sharakhov, Igor V., Wang, Charles, Gowda, Harsha, Tu, Zhijian Jake, Kumar, Ashwani, and Pandey, Akhilesh

Abstract

Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions,192 novel protein start sites,19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted "noncoding RNAs" to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.

Published
2017
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6. Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

Author

Biochemistry, Entomology, Prasad, T. S. Keshava, Mohanty, Ajeet Kumar, Kumar, Manish, Sreenivasamurthy, Sreelakshmi K., Dey, Gourav, Nirujogi, Raja Sekhar, Pinto, Sneha M., Madugundu, Anil K., Pati, Arun H., Advani, Jayshree, Manda, Srikanth S., Gupta, Manoj Kumar, Dwivedi, Sutopa B., Kelkar, Dhanashree S., Hall, Brantley, Jiang, Xiaofang, Peery, Ashley, Rajagopalan, Pavithra, Yelamanchi, Soujanya D., Solanki, Hitendra S., Raja, Remya, Sathe, Gajanan J., Chavan, Sandip, Verma, Renu, Patel, Krishna M., Jain, Ankit P., Syed, Nazia, Datta, Keshava K., Khan, Aafaque Ahmed, Dammalli, Manjunath, Jayaram, Savita, Radhakrishnan, Aneesha, Mitchell, Christopher J., Na, Chan-Hyun, Kumar, Nirbhay, Sinnis, Photini, Sharakhov, Igor V., Wang, Charles, Gowda, Harsha, Tu, Zhijian Jake, Kumar, Ashwani, Pandey, Akhilesh, Biochemistry, Entomology, Prasad, T. S. Keshava, Mohanty, Ajeet Kumar, Kumar, Manish, Sreenivasamurthy, Sreelakshmi K., Dey, Gourav, Nirujogi, Raja Sekhar, Pinto, Sneha M., Madugundu, Anil K., Pati, Arun H., Advani, Jayshree, Manda, Srikanth S., Gupta, Manoj Kumar, Dwivedi, Sutopa B., Kelkar, Dhanashree S., Hall, Brantley, Jiang, Xiaofang, Peery, Ashley, Rajagopalan, Pavithra, Yelamanchi, Soujanya D., Solanki, Hitendra S., Raja, Remya, Sathe, Gajanan J., Chavan, Sandip, Verma, Renu, Patel, Krishna M., Jain, Ankit P., Syed, Nazia, Datta, Keshava K., Khan, Aafaque Ahmed, Dammalli, Manjunath, Jayaram, Savita, Radhakrishnan, Aneesha, Mitchell, Christopher J., Na, Chan-Hyun, Kumar, Nirbhay, Sinnis, Photini, Sharakhov, Igor V., Wang, Charles, Gowda, Harsha, Tu, Zhijian Jake, Kumar, Ashwani, and Pandey, Akhilesh

Abstract

Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions,192 novel protein start sites,19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted "noncoding RNAs" to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.

Published
2017

7. Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

Author

Prasad, T.S. Keshava, primary, Mohanty, Ajeet Kumar, additional, Kumar, Manish, additional, Sreenivasamurthy, Sreelakshmi K., additional, Dey, Gourav, additional, Nirujogi, Raja Sekhar, additional, Pinto, Sneha M., additional, Madugundu, Anil K., additional, Patil, Arun H., additional, Advani, Jayshree, additional, Manda, Srikanth S., additional, Gupta, Manoj Kumar, additional, Dwivedi, Sutopa B., additional, Kelkar, Dhanashree S., additional, Hall, Brantley, additional, Jiang, Xiaofang, additional, Peery, Ashley, additional, Rajagopalan, Pavithra, additional, Yelamanchi, Soujanya D., additional, Solanki, Hitendra S., additional, Raja, Remya, additional, Sathe, Gajanan J., additional, Chavan, Sandip, additional, Verma, Renu, additional, Patel, Krishna M., additional, Jain, Ankit P., additional, Syed, Nazia, additional, Datta, Keshava K., additional, Khan, Aafaque Ahmed, additional, Dammalli, Manjunath, additional, Jayaram, Savita, additional, Radhakrishnan, Aneesha, additional, Mitchell, Christopher J., additional, Na, Chan-Hyun, additional, Kumar, Nirbhay, additional, Sinnis, Photini, additional, Sharakhov, Igor V., additional, Wang, Charles, additional, Gowda, Harsha, additional, Tu, Zhijian, additional, Kumar, Ashwani, additional, and Pandey, Akhilesh, additional

Published
2016
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8. Brain Proteomics of Anopheles gambiae

Author

Dwivedi, Sutopa B., primary, Muthusamy, Babylakshmi, additional, Kumar, Praveen, additional, Kim, Min-Sik, additional, Nirujogi, Raja Sekhar, additional, Getnet, Derese, additional, Ahiakonu, Priscilla, additional, De, Gourav, additional, Nair, Bipin, additional, Gowda, Harsha, additional, Prasad, T.S. Keshava, additional, Kumar, Nirbhay, additional, Pandey, Akhilesh, additional, and Okulate, Mobolaji, additional

Published
2014
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9. Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

Author

Prasad, T.S. Keshava, Mohanty, Ajeet Kumar, Kumar, Manish, Sreenivasamurthy, Sreelakshmi K., Dey, Gourav, Nirujogi, Raja Sekhar, Pinto, Sneha M., Madugundu, Anil K., Patil, Arun H., Advani, Jayshree, Manda, Srikanth S., Gupta, Manoj Kumar, Dwivedi, Sutopa B., Kelkar, Dhanashree S., Hall, Brantley, Jiang, Xiaofang, Peery, Ashley, Rajagopalan, Pavithra, Yelamanchi, Soujanya D., Solanki, Hitendra S., Raja, Remya, Sathe, Gajanan J., Chavan, Sandip, Verma, Renu, Patel, Krishna M., Jain, Ankit P., Syed, Nazia, Datta, Keshava K., Khan, Aafaque Ahmed, Dammalli, Manjunath, Jayaram, Savita, Radhakrishnan, Aneesha, Mitchell, Christopher J., Na, Chan-Hyun, Kumar, Nirbhay, Sinnis, Photini, Sharakhov, Igor V., Wang, Charles, Gowda, Harsha, Tu, Zhijian, Kumar, Ashwani, and Pandey, Akhilesh

Abstract

Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding RNAs” to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anophelinegenomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.

Published
2017
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10. A comprehensive curated resource for follicle stimulating hormone signaling

Author

Telikicherla, Deepthi, primary, Ambekar, Aditi, additional, Palapetta, Shyam Mohan, additional, Dwivedi, Sutopa B, additional, Raju, Rajesh, additional, Sharma, Jyoti, additional, Prasad, TS Keshava, additional, Ramachandra, YL, additional, Mohan, S Sujatha, additional, Maharudraiah, Jagadeesha, additional, Mukherjee, Srabani, additional, and Pandey, Akhilesh, additional

Published
2011
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11. A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry

Author

Chaerkady, Raghothama, primary, Kelkar, Dhanashree S., additional, Muthusamy, Babylakshmi, additional, Kandasamy, Kumaran, additional, Dwivedi, Sutopa B., additional, Sahasrabuddhe, Nandini A., additional, Kim, Min-Sik, additional, Renuse, Santosh, additional, Pinto, Sneha M., additional, Sharma, Rakesh, additional, Pawar, Harsh, additional, Sekhar, Nirujogi Raja, additional, Mohanty, Ajeet Kumar, additional, Getnet, Derese, additional, Yang, Yi, additional, Zhong, Jun, additional, Dash, Aditya P., additional, MacCallum, Robert M., additional, Delanghe, Bernard, additional, Mlambo, Godfree, additional, Kumar, Ashwani, additional, Keshava Prasad, T.S., additional, Okulate, Mobolaji, additional, Kumar, Nirbhay, additional, and Pandey, Akhilesh, additional

Published
2011
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13. A Compendium of Potential Biomarkers of Pancreatic Cancer

Author

Harsha, H. C., primary, Kandasamy, Kumaran, additional, Ranganathan, Prathibha, additional, Rani, Sandhya, additional, Ramabadran, Subhashri, additional, Gollapudi, Sashikanth, additional, Balakrishnan, Lavanya, additional, Dwivedi, Sutopa B., additional, Telikicherla, Deepthi, additional, Selvan, Lakshmi Dhevi N., additional, Goel, Renu, additional, Mathivanan, Suresh, additional, Marimuthu, Arivusudar, additional, Kashyap, Manoj, additional, Vizza, Robert F., additional, Mayer, Robert J., additional, DeCaprio, James A., additional, Srivastava, Sudhir, additional, Hanash, Samir M., additional, Hruban, Ralph H., additional, and Pandey, Akhilesh, additional

Published
2009
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14. Brain proteomics of Anopheles gambiae.

Author

Dwivedi SB, Muthusamy B, Kumar P, Kim MS, Nirujogi RS, Getnet D, Ahiakonu P, De G, Nair B, Gowda H, Prasad TS, Kumar N, Pandey A, and Okulate M

Subjects
Alternative Splicing, Animals, Anopheles genetics, Computational Biology, Female, Genomics, Insect Proteins genetics, Insect Proteins metabolism, Male, Mass Spectrometry, Open Reading Frames, Peptides, Protein Biosynthesis, Proteome, Reading Frames, Reproducibility of Results, Untranslated Regions, Anopheles metabolism, Brain metabolism, Proteomics methods
Abstract

Anopheles gambiae has a well-adapted system for host localization, feeding, and mating behavior, which are all governed by neuronal processes in the brain. However, there are no published reports characterizing the brain proteome to elucidate neuronal signaling mechanisms in the vector. To this end, a large-scale mapping of the brain proteome of An. gambiae was carried out using high resolution tandem mass spectrometry, revealing a repertoire of >1800 proteins, of which 15% could not be assigned any function. A large proportion of the identified proteins were predicted to be involved in diverse biological processes including metabolism, transport, protein synthesis, and olfaction. This study also led to the identification of 10 GPCR classes of proteins, which could govern sensory pathways in mosquitoes. Proteins involved in metabolic and neural processes, chromatin modeling, and synaptic vesicle transport associated with neuronal transmission were predominantly expressed in the brain. Proteogenomic analysis expanded our findings with the identification of 15 novel genes and 71 cases of gene refinements, a subset of which were validated by RT-PCR and sequencing. Overall, our study offers valuable insights into the brain physiology of the vector that could possibly open avenues for intervention strategies for malaria in the future.

Published
2014
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