http://publicationslist.org/data/tkb.gandhi/atom.xml Gandhi Theerthagirihttp://publicationslist.org/tkb.gandhi$basepathfavicon.icoRecent additions to Gandhi Theerthagiri's PublicationsList.org pagehttp://publicationslist.org/publications.png2009-04-07T17:42:59Z http://publicationslist.org/tkb.gandhi/refid1 2009-04-07T17:39:35Z

We present the first analysis of the human proteome with regard to interactions between proteins. We also compare the human interactome with the available interaction datasets from yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans) and fly (Drosophila melanogaster). Of >70,000 binary interactions, only 42 were common to human, worm and fly, and only 16 were common to all four datasets...<br/><br/>T K B Gandhi, Jun Zhong, Suresh Mathivanan, L Karthick, K N Chandrika, S Sujatha Mohan, Salil Sharma, Stefan Pinkert, Shilpa Nagaraju, Balamurugan Periaswamy, Goparani Mishra, Kannabiran Nandakumar, Beiyi Shen, Nandan Deshpande, Rashmi Nayak, Malabika Sarker, Jef D Boeke, Giovanni Parmigiani, Jörg Schultz, Joel S Bader, Akhilesh Pandey (2006) <i>Nat Genet</i> <i></i> <i></i> 38: 3 285-293<br/>

http://publicationslist.org/tkb.gandhi/refid2 2009-04-07T17:39:35Z

BACKGROUND: Protein-protein interaction (PPI) databases have become a major resource for investigating biological networks and pathways in cells. A number of publicly available repositories for human PPIs are currently available. Each of these databases has their own unique features with a large variation in the type and depth of their annotations. RESULTS: We analyzed the major publicly available...<br/><br/>Suresh Mathivanan, Balamurugan Periaswamy, T K B Gandhi, Kumaran Kandasamy, Shubha Suresh, Riaz Mohmood, Y L Ramachandra, Akhilesh Pandey (2006) <i>BMC Bioinformatics</i> <i></i> <i></i> 7 Suppl 5: <br/>

http://publicationslist.org/tkb.gandhi/refid5 2009-04-07T17:40:23Z

Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived protein-protein interactions (>30 000) and PTMs ...<br/><br/>Gopa R Mishra, M Suresh, K Kumaran, N Kannabiran, Shubha Suresh, P Bala, K Shivakumar, N Anuradha, Raghunath Reddy, T Madhan Raghavan, Shalini Menon, G Hanumanthu, Malvika Gupta, Sapna Upendran, Shweta Gupta, M Mahesh, Bincy Jacob, Pinky Mathew, Pritam Chatterjee, K S Arun, Salil Sharma, K N Chandrika, Nandan Deshpande, Kshitish Palvankar, R Raghavnath, R Krishnakanth, Hiren Karathia, B Rekha, Rashmi Nayak, G Vishnupriya, H G Mohan Kumar, M Nagini, G S Sameer Kumar, Rojan Jose, P Deepthi, S Sujatha Mohan, T K B Gandhi, H C Harsha, Krishna S Deshpande, Malabika Sarker, T S Keshava Prasad, Akhilesh Pandey (2006) <i>Nucleic Acids Res</i> <i></i> <i></i> 34: Database issue D411-D414<br/>

http://publicationslist.org/tkb.gandhi/refid7 2009-04-07T17:42:34Z

The data collected by Human Proteome Organization's Plasma Proteome Pilot project phase was analyzed by members of our working group. Accordingly, a functional annotation of the human plasma proteome was carried out. Here, we report the findings of our analyses. First, bioinformatic analyses were undertaken to determine the likely sources of plasma proteins and to develop a protein interaction net...<br/><br/>Peipei Ping, Thomas M Vondriska, Chad J Creighton, T K B Gandhi, Ziping Yang, Rajasree Menon, Min-Seok Kwon, Sang Yun Cho, Garry Drwal, Markus Kellmann, Suraj Peri, Shubha Suresh, Mads Gronborg, Henrik Molina, Raghothama Chaerkady, B Rekha, Arun S Shet, Robert E Gerszten, Haifeng Wu, Mark Raftery, Valerie Wasinger, Peter Schulz-Knappe, Samir M Hanash, Young-Ki Paik, William S Hancock, David J States, Gilbert S Omenn, Akhilesh Pandey (2005) <i>Proteomics</i> <i></i> <i></i> 5: 13 3506-3519<br/>

http://publicationslist.org/tkb.gandhi/refid3 2009-04-07T17:40:23Z

Protein tyrosine phosphatases (PTPs) cooperate with protein tyrosine kinases to regulate signal transduction pathways. Genome-wide surveys cataloging protein tyrosine phosphatases in humans have recently been carried out. Here, we present a bioinformatics analysis of protein tyrosine phosphatases in the human genome to examine their domain architecture, alternative splicing and pseudogenes. We pre...<br/><br/>T K B Gandhi, Sreenath Chandran, Suraj Peri, R Saravana, Ramars Amanchy, T S Keshava Prasad, Akhilesh Pandey (2005) <i>DNA Res</i> <i></i> <i></i> 12: 2 79-89<br/>

http://publicationslist.org/tkb.gandhi/refid4 2009-04-07T17:40:23Z

Plasma is one of the best studied compartments in the human body and serves as an ideal body fluid for the diagnosis of diseases. This report provides a detailed functional annotation of all the plasma proteins identified to date. In all, gene products encoded by 3778 distinct genes were annotated based on proteins previously published in the literature as plasma proteins and the identification of...<br/><br/>Babylakshmi Muthusamy, G Hanumanthu, Shubha Suresh, B Rekha, D Srinivas, L Karthick, B M Vrushabendra, Salil Sharma, Goparani Mishra, Pritam Chatterjee, K S Mangala, H N Shivashankar, K N Chandrika, Nandan Deshpande, M Suresh, N Kannabiran, Vidya Niranjan, Anuradha Nalli, T S Keshava Prasad, K S Arun, Raghunath Reddy, Sreenath Chandran, Trafina Jadhav, D Julie, M Mahesh, S Lynate John, Kshitish Palvankar, D Sudhir, P Bala, N S Rashmi, G Vishnupriya, Kaushik Dhar, S Reshma, Raghothama Chaerkady, T K B Gandhi, H C Harsha, S Sujatha Mohan, Krishna S Deshpande, Malabika Sarker, Akhilesh Pandey (2005) <i>Proteomics</i> <i></i> <i></i> 5: 13 3531-3536<br/>

http://publicationslist.org/tkb.gandhi/refid6 2009-04-07T17:42:34Z

H C Harsha, Shubha Suresh, Ramars Amanchy, Nandan Deshpande, K Shanker, A J Yatish, Babylakshmi Muthusamy, B M Vrushabendra, B P Rashmi, K N Chandrika, N Padma, Salil Sharma, Jose L Badano, M A Ramya, H N Shivashankar, Suraj Peri, Dipanwita Roy Choudhury, M P Kavitha, R Saravana, Vidya Niranjan, T K B Gandhi, Neelanjana Ghosh, Sreenath Chandran, Minal Menezes, Mary Joy, S Sujatha Mohan, Nicholas Katsanis, Krishna S Deshpande, Chaerkady Raghothama, C K Prasad, Akhilesh Pandey (2005) <i>Nat Genet</i> <i></i> <i></i> 37: 4 331-332<br/>

http://publicationslist.org/tkb.gandhi/refid8 2009-04-07T17:42:34Z

The rapid pace at which genomic and proteomic data is being generated necessitates the development of tools and resources for managing data that allow integration of information from disparate sources. The Human Protein Reference Database (http://www.hprd.org) is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein...<br/><br/>Suraj Peri, J Daniel Navarro, Troels Z Kristiansen, Ramars Amanchy, Vineeth Surendranath, Babylakshmi Muthusamy, T K B Gandhi, K N Chandrika, Nandan Deshpande, Shubha Suresh, B P Rashmi, K Shanker, N Padma, Vidya Niranjan, H C Harsha, Naveen Talreja, B M Vrushabendra, M A Ramya, A J Yatish, Mary Joy, H N Shivashankar, M P Kavitha, Minal Menezes, Dipanwita Roy Choudhury, Neelanjana Ghosh, R Saravana, Sreenath Chandran, Sujatha Mohan, Chandra Kiran Jonnalagadda, C K Prasad, Chandan Kumar-Sinha, Krishna S Deshpande, Akhilesh Pandey (2004) <i>Nucleic Acids Res</i> <i></i> <i></i> 32: Database issue D497-D501<br/>

http://publicationslist.org/tkb.gandhi/refid9 2009-04-07T17:42:34Z

Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature ...<br/><br/>Suraj Peri, J Daniel Navarro, Ramars Amanchy, Troels Z Kristiansen, Chandra Kiran Jonnalagadda, Vineeth Surendranath, Vidya Niranjan, Babylakshmi Muthusamy, T K B Gandhi, Mads Gronborg, Nieves Ibarrola, Nandan Deshpande, K Shanker, H N Shivashankar, B P Rashmi, M A Ramya, Zhixing Zhao, K N Chandrika, N Padma, H C Harsha, A J Yatish, M P Kavitha, Minal Menezes, Dipanwita Roy Choudhury, Shubha Suresh, Neelanjana Ghosh, R Saravana, Sreenath Chandran, Subhalakshmi Krishna, Mary Joy, Sanjeev K Anand, V Madavan, Ansamma Joseph, Guang W Wong, William P Schiemann, Stefan N Constantinescu, Lily Huang, Roya Khosravi-Far, Hanno Steen, Muneesh Tewari, Saghi Ghaffari, Gerard C Blobe, Chi V Dang, Joe G N Garcia, Jonathan Pevsner, Ole N Jensen, Peter Roepstorff, Krishna S Deshpande, Arul M Chinnaiyan, Ada Hamosh, Aravinda Chakravarti, Akhilesh Pandey (2003) <i>Genome Res</i> <i></i> <i></i> 13: 10 2363-2371<br/>