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Nagaraj, Shivashankar H. and Reverter, Antonio (2011) A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer. BMC Systems Biology, 5 35.1-35.15. doi:10.1186/1752-0509-5-35 81   14 Cited 19 times in Scopus19 0
Nagaraj, Shivashankar H., Gasser, Robin B. and Ranganathan, Shoba (2007) A hitchhiker's guide to expressed sequence tag (EST) analysis. Briefings in Bioinformatics, 8 1: 6-21. doi:10.1093/bib/bbl015 45   110 Cited 142 times in Scopus142 3
Harsha, H. C., Suresh, Shubha, Amanchy, Ramars, Deshpande, Nandan, Shanker, K., Yatish, A. J., Muthusamy, Babylakshmi, Vrushabendra, B. M., Rashmi, B. P., Chandrika, K. N., Padma, N., Sharma, Salil, Badano, Jose L., Ramya M. A., Nagaraj, S. H., Peri, Suraj, Choudhury, Dipanwita Roy, Kavitha, M. P., Saravana, R., Niranjan, Vidya, Gandhi, T. K. B., Ghosh, Neelanjana, Chandran, Sreenath, Menezes, Minal, Joy, Mary, Mohan, S. Sujatha, Katsanis, Nicholas, Deshpande, Krishna S., Raghothama, Chaerkady, Prasad, C. K. and Pandey, Akhilesh (2005) A manually curated functional annotation of the human X chromosome. Nature Genetics, 37 4: 331-332. doi:10.1038/ng0405-331 73   5 Cited 10 times in Scopus10 0
Shankar, Shiv Hiriyur Nagaraj and Pandey, A. (2002) A novel mode of activating the JAK–STAT signaling pathway. Trends In Biochemical Sciences, 27 7: 336-336. doi:10.1016/S0968-0004(02)02150-3 41   Cited 0 times in Scopus0 0
Fortes, Marina R. S., Reverter, Antonio, Zhang, Yuandan, Collis, Eliza, Nagaraj, Shivashankar H., Jonsson, Nick N., Prayaga, Kishore C., Barris, Wes and Hawken, Rachel J. (2010) Association weight matrix for the genetic dissection of puberty in beef cattle. Proceedings of the National Academy of Sciences of the United States of America, 107 31: 13642-13647. doi:10.1073/pnas.1002044107 176   29 Cited 34 times in Scopus34 0
Ranganathan, Shoba, Nagaraj, Shivashankar H., Hu, Min, Strube, Christina, Schnieder, Thomas and Gasser, Robin B. (2007) A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus. BMC Genomics, 8 5: 311-1-311-13. doi:10.1186/1471-2164-8-311 33   15 Cited 15 times in Scopus15 0
Menzies, Moira, Seim, Inge, Josh, Peter, Nagaraj, Shivashankar H., Lees, Michael, Walpole, Carina, Chopin, Lisa K., Colgrave, Michelle and Ingham, Aaron (2014) Cloning and tissue distribution of novel splice variants of the ovine ghrelin gene. BMC Veterinary Research, 10 1: 211.1-211.9. doi:10.1186/s12917-014-0211-x 12   0 Cited 0 times in Scopus0 0
Peri, Suraj, Navarro, J. Daniel, Amanchy, Ramars, Kristiansen, Troels Z., Jonnalagadda, Chandra Kiran, Surendranath, Vineeth, Niranjan, Vidya, Muthusamy, Babylakshmi, Gandhi, T. K. B., Gronborg, Mads, Ibarrola, Nieves, Deshpande, Nandan, Shanker, K., Shivashankar, H. N., Rashmi, B. P., Ramya M. A., Zhao, Zhixing, Chandrika, K. N., Padma, N., Harsha, H. C., Yatish, A. J., Kavitha, M. P., Menezes, Minal, Choudhury, Dipanwita Roy, Suresh, Shubha, Ghosh, Neelanjana, Saravana, R., Chandran, Sreenath, Krishna, Subhalakshmi, Joy, Mary, Anand, Sanjeev K., Madavan, V., Joseph, Ansamma, Wong, Guang W., Schiemann, William P., Constantinescu, Stefan N., Huang, Lily, Khosravi-Far, Roya, Steen, Hanno, Tewari, Muneesh, Ghaffari, Saghi, Blobe, Gerard C., Dang, Chi V., Garcia, Joe G. N., Pevsner, Jonathan, Jensen, Ole N., Roepstorff, Peter, Deshpande, Krishna S., Chinnaiyan, Arul M., Hamosh, Ada, Chakravarti, Aravinda and Pandey, Akhilesh (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Research, 13 10: 2363-2371. doi:10.1101/gr.1680803 99   603 Cited 621 times in Scopus621 4
Nagaraj, Shivashankar H., Deshpande, Nandan, Gasser, Robin B. and Ranganathan, Shoba (2007) ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform. Nucleic Acids Research, 35 W143-W147. doi:10.1093/nar/gkm378 41   41 Cited 46 times in Scopus46 0
Gotz, Stefan, Garcia-Gomez, Juan Miguel, Terol, Javier, Williams, Tim D., Nagaraj, Shivashankar H., Nueda, María José, Robles, Montserrat, Talon, Manuel, Dopazo, Joaquín and Conesa, Ana (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research, 36 10: 3420-3435. doi:10.1093/nar/gkn176 62   611 Cited 611 times in Scopus611 3
Peri, Suraj, Navarro, J. Daniel, Kristiansen, Troels Z., Amanchy, Ramars, Surendranath, Vineeth, Muthusamy, Babylakshmi, Gandhi, T. K. B., Chandrika, K. N., Deshpande, Nandan, Suresh, Shuba, Rashmi, B. P., Shanker, K., Padma, N., Niranjan, Vidya, Harsha, H. C., Talreja, Naveen, Vrushabendra, B. M., Ramya M. A., Yatish, A. J., Joy, Mary, Shivashankar, H. N., Kavitha, M. P., Menezes, Minal, Choudhury, Dipantha Roy, Ghosh, Neelanjana, Chandran, Sreenath, Mohan, Sujatha, Jonnalagadda, Chandra Kiran, Jonnalagadda, C. K., Prasad, C. K., Kumar-Sinha, Chandan, Deshpande, Krishna S. and Pandey, Akhilesh (2004) Human protein reference database as a discovery resource for proteomics. Nucleic Acids Research, 32 s1: D497-D501. doi:10.1093/nar/gkh070 83   229 Cited 259 times in Scopus259 3
Nagaraj, Shivashankar H., Gasser, Robin B., Nisbet, Alasdair J. and Ranganathan, Shoba (2008). In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): Comparison of the automated ESTExplorer workflow platform with conventional database searches. In: Shoba Ranganathan, Michael Gribskov and Tin Wee Tan, Proceedings: from Sixth International Conference on Bioinformatics (InCoB2007). Asia Pacific Bioinformatics Network (APBioNet) Sixth International Conference on Bioinformatics (InCoB2007), Hong Kong, (S10.1-S10.17). 27-30 August 2007. doi:10.1186/1471-2105-9-S1-S10 34   13 Cited 14 times in Scopus14 0
Nagaraj, Shivashankar H., Gasser, Robin B. and Ranganathan, Shoba (2008) Needles in the EST haystack: Large-scale identification and analysis of excretory-secretory (ES) proteins in parasitic nematodes using expressed sequence tags (ESTs). PLoS Neglected Tropical Diseases, 2 9: e301-1-e301-17. doi:10.1371/journal.pntd.0000301 39   27 Cited 24 times in Scopus24 0
Muthusamy, Babylakshmi, Hanumanthu, G., Suresh, Shubha, Rekha, B., Srinivas, D., Karthick, L., Vrushabendra, B.M., Sharma, Salil, Mishra, Goparani, Chatterjee, Pritam, Mangala, K.S., Shivashankar, H.N., Chandrika, K.N., Deshpande, Nandan, Suresh, M., Kannabiran, N., Niranjan, Vidya, Nalli, Anuradha, Prasad, T.S.Keshava, Arun, K.S., Reddy, Raghunath, Chandran, Sreenath, Jadhav, Trafina, Julie, D., Mahesh, M., John, S. Lynate, Palvankar, Kshitish, Sudhir, D., Bala, P., Rashmi, N.S., Vishnupriya, G., Dhar, Kaushik, Reshma, S., Chaerkady, Raghothama, Gandhi, T.K.B., Harsha, H.C., Mohan, S. Sujatha, Deshpande, Krishna S., Sarker, Malabika and Pandey, Akhilesh (2005) Plasma proteome database as a resource for proteomics research. Proteomics, 5 13: 3531-3536. doi:10.1002/pmic.200401335 37   59 Cited 70 times in Scopus70 0
Kumar, Dhirendra, Yadav, Amit Kumar, Kadimi, Puneet Kumar, Nagaraj, Shivashankar H., Grimmond, Sean M. and Dash, Debasis (2013) Proteogenomic analysis of bradyrhizobium japonicum USDA110 using genosuite, an automated multi-algorithmic pipeline. Molecular and Cellular Proteomics, 12 11: 3388-3397. doi:10.1074/mcp.M112.027169 35   7 Cited 8 times in Scopus8 1
Mulvenna, Jason, Hamilton, Brett, Nagaraj, Shivashankar H., Smyth, Danielle, Loukas, Alex and Gorman, Jeffrey J. (2009) Proteomics analysis of the excretory/secretory component of the blood-feeding stage of the hookworm, Ancylostoma caninum. Molecular and Cellular Proteomics, 8 1: 109-121. doi:10.1074/mcp.M800206-MCP200 39   82 Cited 86 times in Scopus86 0
Reverter, Antonio, Hudson, Nicholas J., Nagaraj, Shivashankar H., Perez-Enciso, Miguel and Dalrymple, Brian P. (2010) Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data. Bioinformatics, 26 7: 896-904. doi:10.1093/bioinformatics/btq051 44   34 Cited 39 times in Scopus39 6
Nagaraj, Shivashankar H., Ingham, Aaron and Reverter, Antonio (2010) The interplay between evolution, regulation and tissue specificity in the Human Hereditary Diseasome. BMC Genomics, 11 Suppl. 4 Article No. S23: . doi:10.1186/1471-2164-11-S4-S23 40   3 Cited 4 times in Scopus4 0
Datu, Bennett J. D., Gasser, Robin B., Nagaraj, Shivashankar H., Ong, Eng K., O'Donoghue, Peter, McInnes, Russell, Ranganathan, Shoba and Loukas, Alex (2008) Transcriptional changes in the hookworm, Ancylostoma caninum, during the transition from a free-living to a parasitic larva. PLoS Neglected Tropical Diseases, 2 1: e130.1-e130.15. doi:10.1371/journal.pntd.0000130 62   39 Cited 46 times in Scopus46 0