List of publications

1. Thennarasu Sugumar, Ganesan Pugalenthi, Murugesan Harishankar and G Dhinakar Raj

(2013) Molecular cloning, sequencing and structural studies of granulocyte–macrophage
colony-stimulating factor (GM-CSF) from Indian water buffalo (Bubalus bubalis).
International Journal of Immunogenetics, doi: 10.1111/iji.12074

2. Khraiwesh B, Pugalenthi G and Fedoroff NV (2013) Identification and Analysis of Red Sea
Mangrove (Avicennia marina) microRNAs by High-Throughput Sequencing and their
Association with Stress Responses. PLoS One. 2013 Apr 8;8(4):e60774.

3. Liang Y, Huimei Hong F, Ganesan Pugalenthi, Jiang S, Jauch R, Stanton LW, Kolatkar PR.
Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor
Zfp206. Nucleic Acids Res. 2012 Jun 26

4. Krishna kumar Kandaswamy,Ganesan Pugalenthi; Kai-Uwe Kalies; Enno Hartmann; Thomas

Martinetz. Prediction of Extracellular matrix proteins based on Random Forest with
maximum relevance minimum redundancy (2013) Journal of Theoretical Biology,
21;317:377-83.

5. Kandaswamy KK, Pugalenthi G, Hazrati MK, Kalies KU, Martinetz T. BLProt: Prediction of
bioluminescent proteins based on support vector machine and relieff feature selection.
BMC Bioinformatics. 2011 Aug 17;12:345.

6. Shameer K, Shingate PN, Manjunath SC, Karthika M, Pugalenthi G, Sowdhamini R. 3DSwap:

curated knowledgebase of proteins involved in 3D domain swapping. Database (Oxford).
2011 Sep 29;2011(0).

7. Kandaswamy, Chou KC, Thomas Martinetz and Kolatkar P. (2011) RSARF: Prediction of
residue solvent accessibility from protein sequence using random forest method. Protein
Pept Lett. 2012 Jan;19(1):50-6.

8. Shameer K, Pugalenthi G, Kandaswamy KK, Sowdhamini R. 3dswap-pred: Prediction of 3D

Domain Swapping from Protein Sequence Using Random Forest Approach. Protein Pept
Lett. 2011 May 19

9. Krishna Kumar Kandaswamy, Kuo-Chen Chou, Thomas Martinetz, Steffen Möller, P. N.

Suganthan, S. Sridharan and Ganesan Pugalenthi (2010) AFP-Pred: A random forest
approach for predicting antifreeze proteins from sequence-derived properties. Journal of
Theoretical Biology , 2011 Feb 7;270(1):56-62.

10. Pugalenthi G, Kandaswamy KK, PN Suganthan, Martinetz T, Sowdhamini R and Kolatkar P.

SMpred: A support vector machine approach to identify structural motifs in protein
structure without using evolutionary information. J Biomol Struct Dyn. 2010 Dec;28
(3):405-14.

11. Krishna Kumar Kandaswamy, Ganesan Pugalenthi, Enno Hartmann, Steffen Möller,
 PN.Suganthan, Prasanna Kolatkar, Thomas Martinetz. Prediction of Apoptosis Protein
Locations with Genetic Algorithms and Support Vector Machines Through a New Mode of
Pseudo Amino Acid Composition. Protein Pept Lett. 2010 Jul 29.

12. Ashish Anand, Ganesan Pugalenthi, Gary B. Fogel, P N Suganthan. An approach for
classification of highly imbalanced data using weighted undersampling. Amino acids 2010.

13. Khader Shameer, G. Pugalenthi, K. Krishna Kumar, P. N. Suganthan, G. Archunan and R.

Sowdhamini (2010) Insights in to protein sequence and structure derived features
mediating 3D domain swapping mechanism using Support Vector Machine based approach
Bioinformatics and Biology Insights 2010 Jun 17;4:33-42.

14. Pugalenthi G, K. Krishna Kumar, PN. Suganthan, G.Archunan and R.Sowdhamini (2010).
LipoPred: Identification of functionally diverse lipocalin proteins from protein sequence
using SVM approach. Amino acids 2010 Aug; 39(3):777-83.

15. K. Krishna Kumar, Pugalenthi G, PN Suganthan and Rajeev Gangal (2010). SVMCRYS: An
SVM approach for the prediction of protein crystallization propensity from protein sequence.
Protein Peptide Letters, Jan 4

16. Kandaswamy KK, Pugalenthi G, Hartmann E, Kalies KU, Möller S, Suganthan PN, Martinetz T.
(2009) SPRED: A machine learning approach for the identification of classical and non-
classical secretory proteins in mammalian genomes. Biochem Biophys Res Commun.
2009 Dec 5

17. Tang K, Pugalenthi G, Suganthan PN, Lanczycki CJ, Chakrabarti S (2009) Prediction of
functionally important sites from protein sequences using sparse kernel least squares
classifiers. Biochem Biophys Res Commun. 2009 Apr 24

18. Pugalenthi G, Ke Tang, PN. Suganthan and Saikat Chakrabarti (2009). Identification of
structurally conserved residues of proteins in absence of structural homologs using neural
network, Bioinformatics 25(2):204-10

19. Pugalenthi G, Kumar KK, Suganthan PN, Gangal R. (2008) Identification of catalytic residues
from protein structure using support vector machine with sequence and structural features.
Biochem Biophys Res Commun. 14; 367(3):630-4

20. K. Krishna Kumar, Pugalenthi G, and PN Suganthan (2009) DNA-Prot: Identification of DNA
binding proteins from protein sequence information using random forest method. Journal
of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 26, Issue Number 6,
(2009)

21. Ashish Anand, Gary B. Fogel, Pugalenthi G and P. N. Suganthan (2008) Prediction of
Transcription Factor Families Using DNA Sequence Features. Lecture Notes in Computer
Science, Pattern Recognition in Bioinformatics

22. Ashish Anand, Pugalenthi G, Gary B. Fogel and P.N. Suganthan. Identification and Analysis
 of Transcription Factor Family-specific Features Derived from DNA and Protein Information.
Pattern Recognition Letters

23. Anand A, Pugalenthi G, Suganthan PN. (2008) Predicting protein structural class by SVM
with class-wise optimized features and decision probabilities. Journal of Theoretical
Biology, 21;253(2):375-80

24. Pugalenthi G, Suganthan PN, Sowdhamini R, Chakrabarti S. (2007). MegaMotifBase: a

database of structural motifs in protein families and superfamilies. Nucleic Acids Res.
2007 Oct 11.

25. Pugalenthi G, Tang K, Suganthan PN, Archunan G, Sowdhamini R. (2007) A machine learning
approach for the identification of odorant binding proteins from sequence-derived
properties. BMC Bioinformatics. 2007 Sep 19;8(1):351

26. Pugalenthi G, Suganthan PN, Sowdhamini R, Chakrabarti S. (2007) SMotif: a server for
structural motifs in proteins. Bioinformatics. 2007 Mar 1;23(5):637-8.

27. Chakrabarti S, Manohari G, Pugalenthi G, Sowdhamini R. (2007) SSToSS-sequence-structural

templates of single-member superfamilies. In Silico Biol.; 6(4):311-9.

28. Pugalenthi G, Shameer K, Srinivasan N, and Sowdhamini R. (2006) HARMONY: an algorithm

for the assessment of protein structures. Nucleic Acids Res. 2006 Jul 1; 34:W231-4.

29. Pugalenthi G, Bhaduri A and Sowdhamini R (2005) iMOTdb - a comprehensive collection of

spatially interacting motifs in proteins. Nucleic Acids Res., 34, D285-286.

30. Chakrabarti S, Anand AP, Bhardwaj N, Pugalenthi G and Sowdhamini R. (2005) SCANMOT:
searching for similar sequences using a simultaneous scan of multiple sequence motifs.
Nucleic Acids Res. 2005 Jul 1; 33:W274-6.

31. Pugalenthi G, Archunan G and Ramanathan Sowdhamini: (2005) DIAL: a web-based server
for the automatic identification of structural domains in proteins. Nucleic Acids Res., 33,
W130-2.

32. Thangudu RR, Vinayagam A, Pugalenthi G, Manonmani A, Offmann B, Sowdhamini R. (2005)

Native and modeled disulfide bonds in proteins: knowledge-based approaches toward
structure prediction of disulfide-rich polypeptides. Proteins. 2005 Mar 1; 58(4):866-79

33. Pugalenthi. G, Bhaduri. A and Sowdhamini R: GenDis: Genome Distribution of Protein

Structural Superfamilies. Nucleic Acids Res., 2005, 33; D252-5.

34. Bhaduri. A, Pugalenthi, G., Gupta, N and Sowdhamini, R.: iMOT: an interactive package for
the selection of spatially interacting motifs in protein. Nucleic Acids Res., 2004, 32,
W602-5.

35. Bhaduri, A., Pugalenthi, G. and Sowdhamini, R. (2004). PASS2: an automated database of
protein alignments organised as structural superfamilies. BMC Bioinformatics 5:35
36. A.Vinayagam, Pugalenthi, G, R.Rajesh and R.Sowdhamini (2004) DSDBASE: A consortium of
native and modelled disulphide bonds in proteins. Nucleic Acid Res., 32(1): D200-2.

37. Vinayagam, A., Shi, J., Pugalenthi. G, Meenakshi, B., Blundell, T.L. and Sowdhamini, R.
(2003). DDBASE2.0: Updated Domain Database with Improved Methods for the
Identification of Structural Domains. Bioinformatics, 19, 1760-1764.