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ORCIDShoba Ranganathan
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- affiliation: Macquarie University, Sydney, Australia
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Journal Articles
- 2021
[j58]Zainab Noor
, Seong Beom Ahn, Mark S. Baker, Shoba Ranganathan, Abidali Mohamedali:
Mass spectrometry-based protein identification in proteomics - a review. Briefings Bioinform. 22(2): 1620-1638 (2021)- 2019
- [j57]Zainab Noor, Jemma X. Wu, Dana Pascovici, Abidali Mohamedali, Mark P. Molloy, Mark S. Baker, Shoba Ranganathan:
iSwathX: an interactive web-based application for extension of DIA peptide reference libraries. Bioinform. 35(3): 538-539 (2019) - [j56]Ari Hardianto, Varun Khanna, Fei Liu, Shoba Ranganathan:
Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε. BMC Bioinform. 19-S(13): 187-197 (2019) - 2018
- [j55]Xinrui Zhou, Jie Zheng, Fransiskus Xaverius Ivan, Rui Yin, Shoba Ranganathan, Vincent T. K. Chow, Chee-Keong Kwoh:
Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses. BMC Genom. 19(S2) (2018) - [j54]Ari Hardianto, Fei Liu, Shoba Ranganathan:
Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA. J. Chem. Inf. Model. 58(2): 511-519 (2018) - 2017
- [j53]Ari Hardianto, Muhammad Yusuf, Fei Liu, Shoba Ranganathan:
Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases. BMC Bioinform. 18(16): 19-30 (2017) - 2016
- [j52]Christian Schönbach, Chandra Verma, Peter J. Bond, Shoba Ranganathan:
Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016). BMC Bioinform. 17(S-19): 87-90 (2016) - 2015
- [j51]Christian Schönbach, Paul Horton, Siu-Ming Yiu, Tin Wee Tan, Shoba Ranganathan:
GIW and InCoB are advancing bioinformatics in the Asia-Pacific. BMC Bioinform. 16(S18): I1 (2015) - [j50]Gopichandran Sowmya, Shoba Ranganathan:
Discrete structural features among interface residue-level classes. BMC Bioinform. 16(S18): S8 (2015) - [j49]Paul Horton, Christian Schönbach, Shoba Ranganathan, Siu-Ming Yiu:
Introduction to selected papers from GIW/InCoB 2015. J. Bioinform. Comput. Biol. 13(5): 1502003:1-1502003:2 (2015) - 2014
- [j48]Shoba Ranganathan, Tin Wee Tan, Christian Schönbach:
InCoB2014: bioinformatics to tackle the data to knowledge challenge. BMC Bioinform. 15(S-16): I1 (2014) - [j47]Shoba Ranganathan, Tin Wee Tan, Christian Schönbach:
InCoB2014: Systems Biology update from the Asia-Pacific. BMC Syst. Biol. 8(S-4): I1 (2014) - 2013
- [j46]Gaurav Kumar, Edmond J. Breen, Shoba Ranganathan:
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. BMC Syst. Biol. 7: 12 (2013) - [j45]Christian Schönbach, Bairong Shen, Tin Wee Tan, Shoba Ranganathan:
InCoB2013 introduces Systems Biology as a major conference theme. BMC Syst. Biol. 7(S-3): S1 (2013) - [j44]Asif M. Khan, Tin Wee Tan, Christian Schönbach, Shoba Ranganathan:
APBioNet - Transforming Bioinformatics in the Asia-Pacific Region. PLoS Comput. Biol. 9(10) (2013) - 2012
- [j43]Christian Schönbach, Sissades Tongsima, Jonathan H. Chan, Vladimir Brusic, Tin Wee Tan, Shoba Ranganathan:
InCoB2012 Conference: from biological data to knowledge to technological breakthroughs. BMC Bioinform. 13(S-17): S1 (2012) - [j42]Ranjeeta Menon, Gagan Garg, Robin B. Gasser, Shoba Ranganathan:
TranSeqAnnotator: large-scale analysis of transcriptomic data. BMC Bioinform. 13(S-17): S24 (2012) - 2011
- [j41]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Database J. Biol. Databases Curation 2011 (2011) - [j40]Javed Mohammed Khan, Harish Reddy Cheruku, Joo Chuan Tong, Shoba Ranganathan:
MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures. Bioinform. 27(8): 1192-1193 (2011) - [j39]Shoba Ranganathan, Christian Schönbach, Janet Kelso, Burkhard Rost, Sheila Nathan, Tin Wee Tan:
Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference. BMC Bioinform. 12(S-13): S1 (2011) - [j38]Varun Khanna, Shoba Ranganathan:
In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance. BMC Bioinform. 12(S-13): S25 (2011) - [j37]Varun Khanna, Shoba Ranganathan:
Structural diversity of biologically interesting datasets: a scaffold analysis approach. J. Cheminformatics 3: 30 (2011) - [j36]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 39(Database-Issue): 7-10 (2011) - 2010
- [j35]Christian Schönbach, Kenta Nakai, Tin Wee Tan, Shoba Ranganathan:
InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. BMC Bioinform. 11(S-7): S1 (2010) - [j34]Gaurav Kumar, Shoba Ranganathan:
Network analysis of human protein location. BMC Bioinform. 11(S-7): S9 (2010) - 2009
- [j33]Shoba Ranganathan:
Towards a career in bioinformatics. BMC Bioinform. 10(S-15): 1 (2009) - [j32]Khar Heng Choo, Tin Wee Tan, Shoba Ranganathan:
A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinform. 10(S-15): 2 (2009) - [j31]Varun Khanna, Shoba Ranganathan:
Physicochemical property space distribution among human metabolites, drugs and toxins. BMC Bioinform. 10(S-15): 10 (2009) - 2008
- [j30]Vladimir Brusic, Shoba Ranganathan:
Critical technologies for bioinformatics. Briefings Bioinform. 9(4): 261-262 (2008) - [j29]Khar Heng Choo, Joo Chuan Tong, Shoba Ranganathan:
Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage. BMC Bioinform. 9(S-1) (2008) - [j28]Lesheng Kong, Shoba Ranganathan:
Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors. BMC Bioinform. 9(S-1) (2008) - [j27]Shivashankar H. Nagaraj, Robin B. Gasser, Alasdair J. Nisbet, Shoba Ranganathan:
In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches. BMC Bioinform. 9(S-1) (2008) - [j26]Shoba Ranganathan, Michael Gribskov, Tin Wee Tan:
Bioinformatics research in the Asia Pacific: a 2007 update. BMC Bioinform. 9(S-1) (2008) - [j25]Khar Heng Choo, Shoba Ranganathan:
Flanking signal and mature peptide residues influence signal peptide cleavage. BMC Bioinform. 9(S-12) (2008) - [j24]Jitendra Gaikwad, Varun Khanna, Subramanyam Vemulpad, Joanne Jamie, Jim Kohen, Shoba Ranganathan:
CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge. BMC Bioinform. 9(S-12) (2008) - [j23]Shoba Ranganathan, Wen-Lian Hsu, Ueng-Cheng Yang, Tin Wee Tan:
Emerging strengths in Asia Pacific bioinformatics. BMC Bioinform. 9(S-12) (2008) - 2007
- [j22]Shivashankar H. Nagaraj, Robin B. Gasser, Shoba Ranganathan:
A hitchhiker's guide to expressed sequence tag (EST) analysis. Briefings Bioinform. 8(1): 6-21 (2007) - [j21]Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan:
Methods and protocols for prediction of immunogenic epitopes. Briefings Bioinform. 8(2): 96-108 (2007) - [j20]Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan:
In silico grouping of peptide/HLA class I complexes using structural interaction characteristics. Bioinform. 23(2): 177-183 (2007) - [j19]Lawrence J. K. Wee, Tin Wee Tan, Shoba Ranganathan:
CASVM: web server for SVM-based prediction of caspase substrates cleavage sites. Bioinform. 23(23): 3241-3243 (2007) - [j18]Kanagasabai Rajaraman, Khar Heng Choo, Shoba Ranganathan, Christopher J. O. Baker:
A Workflow for Mutation Extraction and Structure Annotation. J. Bioinform. Comput. Biol. 5(6): 1319-1337 (2007) - [j17]Shivashankar H. Nagaraj, Nandan Deshpande, Robin B. Gasser, Shoba Ranganathan:
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform. Nucleic Acids Res. 35(Web-Server-Issue): 143-147 (2007) - 2006
- [j16]Joo Chuan Tong, Guanglan Zhang, Tin Wee Tan, J. Thomas August, Vladimir Brusic, Shoba Ranganathan:
Prediction of HLA-DQ3.2ß Ligands: evidence of multiple registers in class II binding peptides. Bioinform. 22(10): 1232-1238 (2006) - [j15]Shoba Ranganathan, Martti Tammi, Michael Gribskov, Tin Wee Tan:
Establishing bioinformatics research in the Asia Pacific. BMC Bioinform. 7(S-5) (2006) - [j14]Joo Chuan Tong, Tin Wee Tan, Animesh A. Sinha, Shoba Ranganathan:
Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris. BMC Bioinform. 7(S-5) (2006) - [j13]Lawrence J. K. Wee, Tin Wee Tan, Shoba Ranganathan:
SVM-based prediction of caspase substrate cleavage sites. BMC Bioinform. 7(S-5) (2006) - [j12]Johann Lenffer, Frank W. Nicholas, Kao Castle, Arjun Rao, Stefan Gregory, Michael Poidinger, Matthew D. Mailman, Shoba Ranganathan:
OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI. Nucleic Acids Res. 34(Database-Issue): 599-601 (2006) - [j11]Durgaprasad Bollina, Bernett T. K. Lee, Tin Wee Tan, Shoba Ranganathan:
ASGS: an alternative splicing graph web service. Nucleic Acids Res. 34(Web-Server-Issue): 444-447 (2006) - 2005
- [j10]Khar Heng Choo, Tin Wee Tan, Shoba Ranganathan:
SPdb - a signal peptide database. BMC Bioinform. 6: 249 (2005) - [j9]Shoba Ranganathan:
Bioinformatics Education - Perspectives and Challenges. PLoS Comput. Biol. 1(6) (2005) - 2004
- [j8]Lesheng Kong, Shoba Ranganathan:
Delineation of modular proteins: Domain boundary prediction from sequence information. Briefings Bioinform. 5(2): 179-192 (2004) - [j7]Bernett T. K. Lee, Tin Wee Tan, Shoba Ranganathan:
DEDB: a database of Drosophila melanogaster exons in splicing graph form. BMC Bioinform. 5: 189 (2004) - [j6]Vivek Gopalan, Tin Wee Tan, Bernett T. K. Lee, Shoba Ranganathan:
Xpro: database of eukaryotic protein-encoding genes. Nucleic Acids Res. 32(Database-Issue): 59-63 (2004) - [j5]Lesheng Kong, Bernett Teck Kwong Lee, Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan:
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins. Nucleic Acids Res. 32(Web-Server-Issue): 356-359 (2004) - 2003
- [j4]Vivek Gopalan, Tin Wee Tan, Shoba Ranganathan:
XdomView: protein domain and exon position visualization. Bioinform. 19(1): 159-160 (2003) - [j3]Kunde Ramamoorthy Govindarajan, Pandjassarame Kangueane, Tin Wee Tan, Shoba Ranganathan:
MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules. Bioinform. 19(2): 309-310 (2003) - [j2]Bernett T. K. Lee, Tin Wee Tan, Shoba Ranganathan:
MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences. Nucleic Acids Res. 31(13): 3533-3536 (2003) - 2001
- [j1]Russ B. Altman, Alfonso Valencia, Satoru Miyano, Shoba Ranganathan:
Challenges for Intelligent Systems in Biology. IEEE Intell. Syst. 16(6): 14-20 (2001)
Conference and Workshop Papers
- 2010
- [c2]Md. Tawhidul Islam, M. Shaikh, Abhaya C. Nayak, Shoba Ranganathan:
Biomarker information extraction tool (BIET) development using natural language processing and machine learning. ICWET 2010: 121-126 - 2005
- [c1]Durgaprasad Bollina, Bernett T. K. Lee, Shoba Ranganathan:
MVC Architecture in Bioinformatics web applications and its Java implementation. iiWAS 2005: 759-764
Editorship
- 2019
- [e3]Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach:
Encyclopedia of Bioinformatics and Computational Biology - Volume 1. Elsevier 2019, ISBN 978-0-12-811432-2 [contents] - [e2]Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach:
Encyclopedia of Bioinformatics and Computational Biology - Volume 2. Elsevier 2019, ISBN 978-0-12-811432-2 [contents] - [e1]Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach:
Encyclopedia of Bioinformatics and Computational Biology - Volume 3. Elsevier 2019, ISBN 978-0-12-811432-2 [contents]
Reference Works
- 2019
- [r8]Dean Southwood, Shoba Ranganathan:
Host-Pathogen Interactions. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 103-112 - [r7]Dean Southwood, Shoba Ranganathan:
Genome Databases and Browsers. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 251-256 - [r6]Amara Jabeen, Abidali Mohamedali, Shoba Ranganathan:
Protocol for Protein Structure Modelling. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 252-272 - [r5]Ari Hardianto, Muhammad Yusuf, Fei Liu, Shoba Ranganathan:
Structure-Based Drug Design Workflow. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 273-282 - [r4]Varun Khanna, Shoba Ranganathan, Nikolai Petrovsky:
Rational Structure-Based Drug Design. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 585-600 - [r3]Zainab Noor, Abidali Mohamedali, Shoba Ranganathan:
Identification of Proteins From Proteomic Analysis. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 855-870 - [r2]Zainab Noor, Subash Adhikari, Shoba Ranganathan, Abidali Mohamedali:
Quantification of Proteins From Proteomic Analysis. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 871-890 - [r1]Shoba Ranganathan:
Preface. Encyclopedia of Bioinformatics and Computational Biology (1) 2019
Coauthor Index
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