Prof H.A.Nagarajaram

ORCID ID: https://orcid.org/0000-0001-8568-0620

Scopus Author ID: 6601967352

Google Scholar ID: https://scholar.google.com/citations?user=SmizLHEAAAAJ&hl=en

Prof. H.A.Nagarajaram is a computational biologist. He was trained under the tutelage of Prof. C. Ramakrishnan (Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India) as his PhD supervisor and his PhD work focused on conformational studies on cyclic peptides and protein structural features. In addition, during his PhD days and he also collaborated with Prof. P. Balaram and Prof. Varadaraja Raghavan. His PhD work and the collaborative works together resulted in publications in the journals such as the International Journal of Peptide and Protein Research, PNAS, FEBS Letters and Journal of Biosciences. 

Soon after his PhD he moved to Prof. Sir Tom Blundell’s laboratory at Birkbeck College, London and later to the Department of Biochemistry, Cambridge University, UK, along with Prof. Blundell. During his stay of four years in Prof. Blundell’s group, he studied the packing of secondary structures among protein families. He determined how the volume of buried amino acid residues is correlated to the packing distances among secondary structural elements. These findings were published in peer-reviewed journals Protein Science and Protein Engineering. He was also involved in collaborative projects where he contributed to the development of homologous superfamily database called HOMSTRAD and also in the development of a side-chain modelling method. These collaborations culminated in publications in the journals such as Structure and Biopolymers.  

In 2000 he returned to India and joined the Centre for DNA Fingerprinting and Diagnostics (CDFD) and established the Laboratory of Computational Biology, which developed into one of the vibrant research groups at CDFD. He was also made the India Node Manager of EMBNet, India Node at CDFD and the Head of the Bioinformatics Facility. Under his headship, the Bioinformatics Facility gained popularity to the extent that M/s Sun Microsystems, in collaboration with the then State Government of Andhra Pradesh, came forward and established one of its global Centre of Excellence in Medical Bioinformatics. Furthermore, he was sent as one of the Indian delegates from DBT to Malaysia to establish cooperation in Biotechnology. He also conducted the first ASEAN-India Bioinformatics workshop, where scientists from the ASEAN countries participated, and this workshop was sponsored by the Ministry of External Affairs, Government of India.

At CDFD, his research group focused on two projects: a) Protein structure prediction and analyses, which culminated in developing methods for protein fold prediction and functional impact of missense mutations and publications in the journals such as Bioinformatics and Human Mutation, and b) Evolution and distribution of simple sequence repeats in bacterial genomes which resulted in the development of databases and publications in the journals such as NAR, Bioinformatics and BMC Genomics. Later, he diversified into systems biology (network biology), focusing on topological aspects of human protein-protein interaction networks. He made seminal discoveries on highly connected proteins (hubs). These works resulted in publications in the journals such as Proteomics, Journal Proteome Research, Bioinformatics and Molecular Biosystems. 

In 2017 he was offered a Professor position by the University of Hyderabad in their prestigious and vibrant School of Life Sciences. In 2018 considering his experience and expertise, he was made the first Head of Department of the newly established Department of Systems and Computational Biology. He was also made the Professor-in-charge of the Centre for Modelling, Simulation and Design (CMSD), which served for three years. 

In the Department of Systems and Computational Biology, School of Life Sciences, his research group is actively pursuing studies on human protein-protein interaction networks under different contexts. His work on Intrinsically disordered regions (IDRs), especially developing substitution scoring matrices for aligning IDRs and studying their evolution, has received broad appreciation. The matrices are now part of the Bioinformatics software suite BIOCONDUCTOR. In addition, he has been part of two international projects on analysing volatile compounds from urine and blood to develop volatile compounds as cancer biomarkers. These projects were in collaboration with a group from NCCS, Pune, University of Madeira, Portugal and Rostock Medical Centre, Germany.  In addition, he is also actively involved in collaborations within the School of Life Sciences. So far, the independent research on human protein interactome and collaborations have resulted in publications in journals such as FEBS Letters, Biochemical Journal, Biomolecular Structure and Dynamics, Computational Biology and Chemistry, etc. 

Under his guidance, eleven students have completed their PhDs, two have submitted their thesis and two are preparing their thesis. One student is currently working for his PhD work. addition, several master's students have done their project work.

He has received extramural funding as PI and Co-PI from DBT, DST, CSIR, and also some private companies. He was part of mega projects such as CSIR’s NMITLI. Currently leading two mega projects: a) DBT Centre for Microbial Informatics (DBT-CMI), funded by DBT’s BTISNet and b) Developing and implementing the University of Hyderabad-IoE-ODA Centre for Translation Research -UNITE from the Institute of Eminence grant of the University of Hyderabad.

The DBT-CMI has entered into an MoU with Anthropological Survey of India (AnSI) in the metagenome analysis of gut microbiomes of some tribal communities  of India (please click for details). 

1. Structural and functional impacts of Human proteins harboring disease mutations: We have been exploring how known disease-causing mutations impact protein structure, hence, their molecular functions and further, their interactions with the other biomolecules. Our past studies resulted in the development of a computational tool called HANSA for prediction of functional impact of disease-causing missense mutations in human proteins. We were part of collaborative studies where we had investigated effects of several disease-causing mutations on the protein harboring them. Currently we are investigating Loss-of-Function as well as Gain-of-Function mutations in human proteins.
2. Molecular properties of centrally important proteins in protein-protein interaction networks: Protein-protein interaction networks are characterized by the presence of few proteins with high degree, betweenness and other centrality values. When tissue-specific protein-protein interactions were analysed we could find a dichotomy among the highly connected proteins (hubs). Some of the highly connected proteins are expressed in very tissues and cell types and hence designated as “local hubs” and some others are universally expressed in most of the tissues and hence were designated as “global hubs”. These two categories of proteins show distinct molecular and functional proteins. Similarly, we also found trichotomy among the proteins with high degree and high betweenness values which we referred to as pure-hubs, pure-bottlenecks and hub-bottlenecks  
3. Metagenome analyses of environmental microbiomes: We investigate relationships between microbiome profiles and their habitats. We are currently analyzing metagenomes of the human gut microbiota. We are also analyzing marine microbiomes. The analyses include microbial diversities, co-existing microbial communities and their functional biopathways.
4. Simple sequence repeats in bacterial genomes:  Known bacterial whole genomes were screened for abundance, distribution and polymorphism of simple sequence repeats (SSRs; also referred to as microsatellites). During the course of our studies we developed widely used and cited tool (referred to as IMEx (Imperfect Microsatellite Extractor)) and databases MICdb (Microsatellite Database) and  PSSRdb (Polymorphic Simple Sequene Repeats database). 

Current Teaching Schedule at the University of Hyderabad

Even semesters: Computational Systems Biology (Two units pertaining to Biological Networks) – 2 Credits to Integrated Master of Science (IMSc) Systems Biology and Master of Technology (MTech) Bioinformatics Students.

Odd semesters: Basics of Mathematics and Statistics (2 credits) – for MTech Bioinformatics and MSc (Biotechnology) students.

In addition, Bio-Statistics (2 credits)  a part of the four credit Research Methodology course for Pre-PhD students.

Past Teaching Experience:

Before joining the university as a professor, as a Group Leader and Scientist, in the Centre for DNA Fingerprinting and Diagnostics (CDFD), he was participating in several teaching programs that included Bioinformatics and Computational Biology courses in and outside CDFD.  In CDFD, as a part of mandatory bridge courses for fresh PhD students, I used to take basic as well as an advance courses in Bioinformatics and Computational Biology covering biological sequence analysis, biomolecular structural analysis, and biological networks and their analysis. 

He also worked as a guest faculty for the following universities:

(a)  Osmania University, Hyderabad - He used to teach two complete papers for the students of Post-graduate diploma in Bioinformatics and computational structural biology. 

(b)  University of Hyderabad (before joining this university)- He used to teach the Bioinformatics course (3 +2 credits) for the students of M.Tech. (Bioinformatics)

(c)  Acharya N.G.Ranga Agricultural Univeristy, Hyderabad - He used to take a course on Bioinformatics for the students of M.Sc.(Agricultural Biotechnology).

1. Saratchandra Singh Khumukcham, Vasudevarao Penugurti, Suresh Bugide, Anju Dwivedi, Anita Kumari, P.S. Kesavan, Sruchytha Kalali, Yasaswi Gayatri Mishra, Vakkalagadda A. Ramesh, Hampapathalu A. Nagarajaram, Aprotim Mazumder, Bramanandam Manavathi (2023) HPIP and RUFY3 are non-canonical guanine exchange factors of Rab5 to regulate endocytosis-coupled focal adhesion turnover,  J. Biol. Chem.https://doi.org/10.1016/j.jbc.2023.105311 (Oct, 2023)
2. Nithya, C., Manjari Kiran & H.A.Nagarajaram (2023) Hubs and Bottlenecks in Protein-Protein Interaction Networks in “Methods Molecular Biology”, Vol. 2719, Sudip Mandal (Eds): “Reverse Engineering of Regulatory Networks” https://doi.org/10.1007/978-1-0716-3461-5_13, pages 227-248
3. Nilisha Rastogi, Sheeba Zarin, Anwar Alam, Guruprasad Varma Konduru, P. Manjunath, Abhay Mishra, Saroj Kumar, Hampapathalu Adimurthy Nagarajaram, Seyed Ehtesham Hasnain, Nasreen Zafar Ehtesham (2023) Structural and biophysical properties of therapeutically important proteins Rv1509 and Rv2231A of Mycobacterium tuberculosis Int. J.Biol.Macromol. 245, 125455 (Aug 1 2023)
4. Nithya, C., Manjari Kiran & H.A.Nagarajaram (2023) Dissection of Hubs and Bottlenecks in Human Protein-Protein Interaction Network Comp. Biol & Chemistry 102,  https://doi.org/10.1016/j.compbiolchem.2022.107802 (01 Feb 2023
5. Rakesh Trivedi & H.A.Nagarajaram (2022) Intrinsically Disordered Proteins: An Overview Int. J. Mol. Sci.  23, 14050. https://doi.org/10.3390/ijms232214050 (14 Nov 2022)
6. Guruprasad Varma Konduru & Hampapathalu Adimurthy Nagarajaram (2022) Human TMPRSS2 non-catalytic ectodomain and SARS-CoV-2 S2' subunit interaction mediated SARS-CoV-2 endocytosis: a model proposal with virtual screening for potential drug molecules to inhibit this interaction, Journal of Biomolecular Structure and Dynamics  41 (13), 6422-6433 DOI: 10.1080/07391102.2022.2105956 (31 July 2022)
7. Ajay K Chaudhary, Aishwarya Gholse, H.A. Nagarajaram, Ashwin B Dalal, Neerja Gupta, Atanu K Dutta, Sumita Danda, Rekha Gupta, V H Sankar, Gandham SriLakshmi Bhavani, Katta M Girisha, , Sobha R Phadke, Prajnya Ranganath and Murali Dharan Bashyam (2022) Ectodysplasin pathogenic variants affecting the furin-cleavage site and unusual clinical features define X-linked hypohidrotic ectodermal dysplasia in India Am J Med Genet Part A 188, 788-805 (01 Dec 2021)
8. Seera, S and Nagarajaram HA (2022)  Effect of Disease Causing Mutations on Intrinsically Disordered Regions in Proteins Protein and Peptide Letters 29, 254-267 (date 22 March 2022
9. Trivedi R, Nagarajaram HA (2020) Substitution Scoring Matrices for Proteins - An Overview. Protein Science 29, 2150-2163 
10. Hari Parapatla, Ramurthy Gudla, Guruprasad Varma Konduru, Elsin Raju Devadasu,. Hampapathula Adimurthy Nagarajaram, Manjula Sritharan, Rajagopal Subramanyam and Dayananda Siddavattam (2020) Organophosphate hydrolase interacts with ferric-enterobactin and promotes iron uptake in association with TonB dependent transport system Biochemical Journal 477 2821-2840
11. Ravindra Taware, Khushman Taunk, T. V.Santosh Kumar, Jorge A. M. Pereira, José S. Câmara, H. A. Nagarajaram, Gopal Chandra Kundu, Srikanth Rapole (2020) Extracellular volatilomic alterations induced by hypoxia in breast cancer cells Metabolomics 16, 21
12. Trivedi, R., Nagarajaram, H.A. (2019) Amino acid substitution scoring matrices specific to intrinsically disordered regions in proteins. Sci Rep 9, 16380 doi:10.1038/s41598-019-52532-8
13. Ramurthy Gudla1, Guruprasad Varma Konduru2, Hampapathalu Adimurty Nagarajaram3, and Dayananda Siddavattam* (2019) Organophosphate hydrolase interacts with Ton components and targets membrane only in presence of ExbB/ExbD complex. FEBS Letters 593 581-593
14. Ravindra Taware, Khushman Taunk, Jorge Pereira, Amey Shirolkar, Dharmesh Soneji , José S Câmara, H A Nagarajaram, Srikanth Rapole**  (2018) Volatilomic insight of head and neck cancer via the effects observed on saliva metabolites Scientific Reports 8:17725 | DOI:10.1038/s
15. Khushman Taunk, RavindraTaware, Tushar H. More, Priscilla Porto-Figueira, Jorge Pereira, Rajkishore Mohapatra, Dharmesh Soneji , José S Câmara, H A Nagarajaram, Srikanth Rapole**  (2018) A non-invasive approach to explore the discriminatory potential of the urinary volatome of invasive ductal carcinoma of the breast RSC Advances 8, 25040-25050
16. Carina Cavaco, Jorge Pereira, Khushman Taunk, Ravindra Taware, Srikanth Rapole, Hampapathalu Nagarajaram and José S. Câmara** (2018) Screening of salivary volatiles for putative breast cancer discrimination: An exploratory study involving geographic distant populations Analytical and Bioanalytical Chemistry, 410, 4459-4468
17. Taware,  Khushman Taunk, Jorge A. M. Pereira, Rahul Dhakne, Narayanan Kannan,  Dharmesh Soneji, José S. Câmara,  H A Nagarajaram,  Srikanth Rapole** (2017) Investigation of urinary volatomic alterations in head and neck cancer: A non-invasive approach towards diagnosis and prognosi Metabolomics 13, 111 (DOI 10.1007/s11306-017-1251-6)
18. Kumar, Parveen; Munnangi, Prathyusha; Chowdary, KVS; Shah, Varun; Shinde, Swapnil; Kolli, Nanci; Halehalli, Rachita; Nagarajaram, Hampapathalu; Maddika, Subbareddy (2017)  A human tyrosine phosphatase interactome mapped by proteomic profiling J. Proteome Res. 16,  2789–2801
19.  Manjari Kiran and H.A.Nagarajaram** (2016) Interaction and Localization Diversities of Global and Local Hubs in Human Protein­‐Protein Interaction Network Molecular Biosystems 12, 2875 – 2882
20. A K Chaudhary, R Mohapatra, H A Nagarajaram, P Ranganath, A Dalal, A Dutta, S Danda, K Girisha, M D Bashyam** (2015). The novel missense EDAR p.L397H mutation causes autosomal dominant hypohidrotic ectodermal dysplasia. Journal of european academy of dermatology and venearology 31, (doi.org/10.1111/jdv.13587
21. Radha Rama Devi A**, Ramesh V.A, Nagarajaram H.A, SatishS.P.S, Jayanthi U, Lokesh Lingappa (2015) Spectrum of Mutations in Glutaryl-CoA Dehydrogenase gene in GlutaricAciduria Type I - Study from South India Brain & Development DOI: http://dx.doi.org/10.1016/j.braindev.2015.05.013
22. Abdul Mueed Bidcho, Ashwin Dalal, Rakesh Trivedi, Anju Shukla, Sheela Nampoothiri, VH Sankar, Sumita Danda, Neerja Gupta, Madhulika Kabra, Shrikiran A Hebbar, Ramesh Y Bhat, Divya Matta, Alka V Ekbote, Ratna Dua Puri, Shubha R Phadke, Kalpana Gowrishankar, Shagun Aggarwal , Prajnya Ranganath, Sheetal Sharda, Mahesh Kamate, Chaitanya A Datar, Kamalakshi Bhat, Nutan Kamath, Puthiya Mundyat Gopinath, Ishwar C Verma, HA Nagarajaram, Kapaettu Satyamoorthy, Katta Mohan Girisha** (2015) Recurrent and novel GLB1 mutations in India Gene 567, 173-181
23. 21.  Jorge Pereira**, Priscilla Porto-Figueira, Carina Cavaco, Khushman 
    Taunk, Srikanth  Rapole, Rahul Dhakne, Hampapathalu Nagarajaram, José Câmara (2015) Breath analysis as a potential and non-invasive frontier in disease diagnosis. A metabolomic approach. Metabolites 5, 3-55
24. Rachita Halehalli and H.A.Nagarajaram** (2015) Molecular principles of human virus protein-protein interactions Bioinformatics 31, 1025-1033
25. Anupam Sinha and H.A. Nagarajaram** (2014) Nodes occupying central positions in human tissue specific PPI networks are enriched with many splice variants. Proteomics 14, 2242-2248
26. Siddaramappa J Patil, Gaurava Kumar Rai, Venkatraman Bhat, Vakkalagadda A Ramesh, H A Nagarajaram, Jyoti Matalia, Shubha R Phadke (2014) Distal Arthrogryposis Type 5D With A Novel ECEL1 Gene Mutation Am J Med Genet Part A DOI: 10.1002/ajmg.a.36702 
27. Abdul Mueed Bidchol, Ashwin Dalal, Hitesh Shah, Suryanarayana S, Sheela Nampoothiri, Madhulika Kabra, Neerja Gupta, Sumita Danda, Kalpana Gowrishankar, Shubha R Phadke, Seema Kapoor, Mahesh Kamate, IC Verma, Ratna Dua Puri, VH Sankar, A Radha Rama Devi, SJ Patil, Prajnya Ranganath, S Jamal Md Nurul Jain, Meenal Agarwal, Ankur Singh,  Pallavi Mishra, Parag M Tamhankar, Puthiya Mundyat Gopinath, Nagarajaram HA, Kapaettu Satyamoorthy, Katta Mohan Girisha (2014) GALNS Mutations in Indian Patients with Mucopolysaccharidosis IVA  Am J Med Genet Part A https://doi.org/10.1002/ajmg.a.36735
28. Rachita Halehalli and H.A.Nagarajaram** (2014) Viral proteins that bridge unconnected proteins and components in human PPI network Mol.Bio.Sys. 10, 2448-2458
29. Anusha Uttarilli, Prajnya Ranganath, S. Jamal Md Nurul Jain, Krishna Prasad C, Anupam Sinha, Ishwar C Verma, Shubha R Phadke, Ratna D Puri, Sumita Danda, Mamta N Muranjan, Ganesh Jevalikar, H A Nagarajaram, Ashwin B Dalal**(2014) Novel mutations of the ARSB gene in Indian patients with Mucopolysaccharidosis Type VI Indian J. Med. Red. 142, 414-425
30. Murali D. Bashyam**, Ajay K. Chaudhary, Manjari Sinha, H. A. Nagarajaram et al (2014) Splice, insertion-deletion and nonsense mutations that perturb the Phenylalanine hydroxylase transcript cause Phenylketonuria in India. J.Cell.Biochem.  115:566-574
31. Suresh B. Mudunuri,  S. Patnana and H.A. Nagarajaram** (2014) MICdb3.0:  A Comprehensive Resource of Microsatellite Repeats from Prokaryotic Genomes Database doi:10.1093/database/bau005
32. Murali D. Bashyam, Ajay K. Chaudhary, Manjari Kiran, Venkat Reddy, Hampapathalu A. Nagarajaram, Ashwin Dalal, Leena Bashyam, Deepti Suri, Anju Gupta, Neerja Gupta, Madhulika Kabra, Ratna Puri, RadhaRamaDevi, Seema Kapoor, Sumita Danda. Molecular analyses of novel ASAH1 mutations causing Farber lipogranulomatosis: analyses of exonic splicing enhancer inactivating mutation. Clin Genet,2014; 86:530-538.
33. Manjari Sinha and H.A.Nagarajaram** (2013) Global versus local hubs in human protein-protein interaction network J.Proteome Res. 12: 5436–5446
34. Anupam Sinha and H.A.Nagarajaram** (2013) Effect of Alternative Splicing on the Degree Centrality of nodes in PPI networks of Homo sapiens J.Proteome Res. 12: 1980–1988
35. Vishal Acharya and H.A.Nagarajaram** (2013) Response to: Statistical Analysis of Missense Mutation Classifiers Human Mutat 34 407
36. Suresh B. Mudunuri**, Priyatosh Mishra, and Nagarajaram, H.A. (2012) "In Silico Survey of Distribution and Frequency of Imperfect Microsatellite Repeats in Viral Genomes.", Proceedings of IEEE International Conference on Data Science & Engineering (ICDSE), 2012 Vol. 1, pp. 31-36 
37. Murali D Bashyam**, Ajay K Chaudhary, Manjari, H A Nagarajaram, A Radha Rama Devi, Leena Bashyam, E Chandrakanth Reddy, Ashwin Dalal (2012). Molecular genetic analysis of MSUD from India reveals mutations causing altered protein truncation affecting the C-termini of E1α and E1β. Journal of Cellular Biochemistry113:3122-3132
38. Murali Bashyam**, Guroji Purushotham, Ajay K Chaudhary, Madhumohan Rao, Vishal Acharya, Tabrez Mohammad, H. A. Nagarajaram, Vuppaladadhiam Hariram, Calambur Narasimhan (2012) A low prevalence of MYH7/MYBPC3 mutations among Familial Hypertrophic Cardiomyopathy patients in India. Mol Cell Biochem. 360:373-382
39. M D Bashyam**, A K Chaudhary, E C Reddy, V Reddy, V Acharya, H A Nagarajaram (2012), A R R Devi, L Bashyam, A B Dalal, N Gupta, M Kabra, M Agarwal, S R Phadke, R Tainwala, R Kumar, S V Hariharan. An Ectodysplasin A receptor (EDAR) founder mutation results in a high frequency of the autosomal recessive form of Hypohidrotic Ectodermal Dysplasia in India. Br J Dermatol. 166:819-8
40. Kumar and H.A.Nagarajaram** (2012) A Study on Mutational Dynamics of Simple Sequence Repeats in Relation to Mismatch Repair System in Prokaryotic Genomes J. Mol. Evol. 74 127-139 
41. Suresh B. Mudunuri**, Priyatosh Mishra, and Nagarajaram, H.A. (2012) "Distributional Analysis and Motif Frequencies of Compound Microsatellite Repeats in Viral Genomes.", Proceedings of IEEE International Conference on Computing, Electronics and Electrical Technologies (ICCEET), 2012, vol.1, pp.887-893
42. Vishal Acharya and H.A.Nagarajaram** (2012) Hansa: An automated method for discriminating disease and neutral human nsSNPs Hum Mutat 33 332-337 
43. Md. Tabrez Shamim and H A Nagarajaram** (2011) A Hierarchical Approach to Protein Fold Recognition J. Integr. Bioinform. 8:185
44. Murali Bashyam**, Guroji Purushotham, Ajay K Chaudhary, Madhumohan Rao, Vishal Acharya, Tabrez Mohammad, H. A. Nagarajaram, Vuppaladadhiam Hariram, Calambur Narasimhan (2012) A low prevalence of MYH7/MYBPC3 mutations among Familial Hypertrophic Cardiomyopathy patients in India. Mol Cell Biochem.  360:373-382
45. Md. Tabrez Shamim and H.A. Nagarajaram** (2011) SVM-Based method for protein structural class prediction using secondary structural content and structural information of amino acids J.Bioinform. Comput. Biol DOI: 10.1142/ S02197200 11005422
46. Pankaj Kumar, P. S. Chitanya and H A Nagarajaram** (2011) PSSRdb: A Relational Database of Polymorphic Simple Sequence Repeats Extracted from Prokaryotic Genomes Nucleic Acid Res. 39(suppl 1): D601-D605  
47. Suresh B Mudunuri, Pankaj Kumar, Allam Appa Rao, S Pallamsetty and H A Nagarajaram** (2010) G-IMEx: A comprehensive software tool for detection of microsatellites from genome sequences Bioinformation 5: 221-223 
48. G Purushotham, K Madhumohan, Mohammad Anwaruddin, H.A.Nagarajaram, Vuppaladadhiam Hariram,Calambur Narasimhan,Murali D Bashyam** (2010) The MYH7 p.R787H mutation causes hypertrophic cardiomyopathy in two unrealted families.Exp clin Cardial 2010;15(1):e1-e4. 
49.  Suresh, M., Rao, A.A., Mishra, P. and H.A. Nagarajaram** (2010) Comparative Analysis of Microsatellite Detecting Software: A Significant Variation in Results and Influence of Parameters, Proceedings of International Symposium on Biocomputing, (ISB 2010), Kerala, February 15-17, 2010. (Link to ACM Digital Library) 
50. Suresh B. Mudunuri**, Allam Appa Rao, S Pallamsetty, Priyatosh Mishra and H.A.Nagarajaram (2009) VMD: Viral Microsatellite Database - A Comprehensive Resource for All Viral Microsatellites. Journal of Computer Science and Systems Biology. 22: 283-000. 
51. Korupolu, R.V., Achary, M.S., Aneesa, F., Sathish, K., Wasia, R., Sairam, M., Nagarajaram, H.A. and Singh, S.S** (2009) Profilin oligomerization and its effect on poly (l-proline) binding and phosphorylation  Int. J.Biol.Macromol. 45: 265-273
52. Achary, M.S. and H.A. Nagarajaram** (2009) Effects of Disease Causing Mutations on the Essential Motions in Proteins J.Biomol. Struct. Dyn. 26: 609-624 
53. Achary, M.S. and H.A. Nagarajaram** (2008) Comparative docking studies of CYP1b1 and its PCG associated mutant forms J. Biosci. 33: 699–713
54. Md. Tabrez Anwar Shamim, Mohammad Anwaruddin and H. A. Nagarajaram**
    (2007) Support Vector Machine based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs. Bioinformatics 23:3320-3327
55. Suresh, M and H.A.Nagarajaram** (2007) IMEx: Imperfect Microsatellite Extractor Bioinformatics 23:1181-7
56. The NMITLI-BioSuite Team (….H.A. Nagarajaram.) (2007) BioSuite: A comprehensive bioinformatics software package (A unique industry–academia collaboration) Curr. Sci. 92: 29-38
57. Sreenu,V.B.,  Kumar, P., Nagaraju, J. and H.A. Nagarajaram** (2007) Simple sequence repeats in mycobacterial genomes J.Biosci. (A peer-reviewed special issue on Computational Biology) 32: 1-15
58. M.S. Achary, A. B.M. Reddy, S. Chakrabarti, S.G. Panicker, A.K. Mandal, N.Ahmed, D. Balasubramanian, S.E. Hasnain, and H.A.Nagarajaram** (2006) Disease Causing Mutations in Proteins: Structural Analysis of the CYP1b1 Mutations Causing Primary Congenital Glaucoma in Humans Biophysical J. 91: 4329-4339
59. Sreenu,V.B.,  Kumar, P., Nagaraju, J. and H.A. Nagarajaram** (2006) Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: Implications on genome evolution and plasticity BMC Genomics 7:78-88 (Highly accessed article)
60.  Cheeran, A., Suganthan, R.B., Swapna, G., Bandey, I., Acharya, S., Nagarajaram, H.A. and Sen. R** (2005) E. coli RNA polymerase mutations located near the upstream edge of RNA:DNA hybrid and the beginning of the RNA exit channel are defective for transcription antitermination by N protein from lambdoid phage H-19B J.Mol. Biol 352:  28-43
61. Prasad,M.D., Muthulakshmi,M., Arunkumar,K.P., Madhu,M., Sreenu,V.B., Pavithra,V., Bose,B., Nagarajaram,H.A., Mita,K., Shimada, T. and Nagaraju, J**(2005) SilkSatDb: A microsatellite database of the silkworm, Bombyx mori. Nucleic Acids Research. 33: D403-D406
62. H.A.Nagarajaram ,Prathima Iengar and Indira Ghosh** (2005) In silico approach to antimalarial drug discovery: Design of selective inhibitor to Plasmodium falciparum aspartic proteases Frontiers in Biophysics168-181.
63.  Ahmed Kamal**, G. Ramesh, O. Srinivas, P. Ramulu, N. Laxman ,Tasneem Rehana, M.Deepak, M.S. Achary and H. A. Nagarajaram (2004). Design, Synthesis, and Evaluation of Mixed Imine-Amine Pyrrolobenzodiazepine Dimers with Efficient DNA-Binding Affinity and Potent Cytotoxicity Bio-organic & Medicinal Chemistry 12:5427-5436. 
64. Sreenu, V.B., Ranjitkumar, G., Swaminathan, S., Priya, S., Bose, B., Narendra Pavan, M., Nagaraju, J., H.A.Nagarajaram** (2004) MICdb - Database of Prokaryotic Microsatellites. Nucleic Acids Research Published in online database issue. 
65. Majeed, A.A., Ahmed, N., Rao, K.R., Ghousunnissa, S., Kausar, F., Bose, B., H.A. Nagarajaram, Katoch, V.M., Cousins, D.V., Sechi, L.A., Gilman, R.H. and Hasnain, S.E** (2004) AmpliBASE MTTM: A Mycobacterium tuberculosis diversity knowledgebase. Bioinformatics 20:989-92.
66. V.B.Sreenu, G.Ranjitkumar, S.Swaminathan, S.Priya, B.Bose, M.N.Pavan, Geetha Thanu, J.Nagaraju and H.A.Nagarajaram** (2003) MICAS: A fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences. Applied Bioinformatics 2(3) 165-168. 
67.  V.B.Sreenu, Vishwanath Alevoor, J.Nagaraju and H.A.Nagarajaram** (2003) MICdb: Database of Prokaryotic Microsatellites Nucleic Acids Research 31 106-108. 
68. A.Kamal**, N. Laxman, G. Ramesh, P. Ramulu, O. Srinivas, K. Neelima, A. K. Kondapi, V. B. Sreenu and H.A.Nagarajaram (2002) Design, synthesis, and 1991evaluation of new non-cross linking pyrrolobenzodiazepine dimers with efficient DNA-binding ability and potent antitumour activity J. Med. Chem45 4679-4688. 
69.  E.Narayanan, H.A.Nagarajaram, C. Ramakrishnan and N.Srinivasan** (2002) Influence of solvent molecules on the stereochemical code of glycine residue PROTEINS 49 326-334. 
70. S.G.Panicker**, A.B.M.Reddy, A.K.Mandal,N.Ahmed, H.A.Nagarajaram, S.E.Hasnain and D.B. Balasubramanian (2002) Identification of novel mutations causing familial primary congenital glaucoma in  indian pedigrees Investigative Ophthalmology & Visual Science 43 1358-1366 2002.  
71. J. Mendes, H.A. Nagarajaram, Cláudio M. Soares, Tom L. Blundell, Maria Arménia Carrondo** (2001). Incorporating knowledge-based biases into an energy-based  side-chain   modeling method: application to comparative modeling of protein structure Biopolymers 59:2 72-86.
72. N. Campillo**, H.A. Nagarajaram & I. Ghosh (2001). Phosphoribosyltransferase superfamily: A comparative structural analysis J.Mol.Model. 7 80-89. 
73. D.F.Burke@, C.Dean@, H.A.Nagarajaram@, ... , Tom L.Blundell** and  K.Mizuguchi** (1999).  An iterative structure-assisted approach to sequence alignment and comparative modeling PROTEINS 3 55-60.  @joint first authors.
74. H.A.Nagarajaram, B.V.B.Reddy and Tom L. Blundell** (1999).  Analysis and prediction of inter-strand packing distances between beta-sheets of globular proteins. Protein Eng. 12 1055-1062.
75. B.V.B.Reddy, H.A.Nagarajaram and Tom L. Blundell** (1999).  Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins Protein Sci. 8 573-586.
76. R.Sowdhamini, D.F.Burke, Jing-Fei Huang, K.Mizuguchi, H.A.Nagarajaram, N.Srinivasan, R.E.Stewart and Tom L. Blundell** (1998). CAMPASS: A database of structurally aligned protein superfamilies Structure 61087-1094.
77. K.Gunasekaran, H.A.Nagarajaram, C. Ramakrishnan and P. Balaram** (1998) Stereochemical punctuation marks in protein structures: Glycine and Proline containing helix stop signals J.Mol.Biol. 275 917-932.
78. R.Sowdhamini, D. F. Burke, C. Deane, Jing-Fei Huang, K.Mizuguchi, H.A.Nagarajaram, J.P.Overington, N.Srinivasan, R.E.Steward and Tom L.Blundell** (1998).  Protein 3D structural databases: Domains, structurally aligned homologues and superfamilies  Acta Crystallogr. D54 1168-1177.
79. R.Varadarajan**, H.A.Nagarajaram and C. Ramakrishnan (1996) A procedure for the prediction of temperature-sensitive mutants of a globular protein based solely on the amino acid sequence  Proc. Natl. Acad. Sci. (USA) 93 13908-13913.
80. H.A.Nagarajaram and C. Ramakrishnan** (1995)  Stereochemical studies on cyclic peptides - Detailed energy minimisation studies on hydrogen bonded all-trans cyclic pentapeptide backbones J.Biosci. 20 591-611.
81. H.A.Nagarajaram, R.Sowdhamini, C.Ramakrishnan and P.Balaram** (1993) Termination of right handed helices in proteins by the residues in left handed helical conformation FEBS letters 321 79-83.
82. H.A.Nagarajaram, P.K.Paul, K. Ramanarayanan, K.V.Soman  and C. Ramakrishnan** (1992) Conformational studies on beta-bends containing a cis peptide unit Int. J. Peptides Proteins Res. 40 383-394.
83. H.A.Nagarajaram and C. Ramakrishnan** (1991) Energy minimisation studies on cyclic pentapeptides Indian J. Phys. 65B 449-454.

Invited Articles :

1. Anupam Sinha and H.A.Nagarajaram** (2011) Studies on Protein-Protein Interactions: A New Frontier in Computational Biology in “Proceedings of 2nd International Conference on Metacomputing” Editor:Dr. P.K.Roy,  Allied Publishers Pvt. Ltd., New Delhi
2. R.K.Gundu, B.Bose, S.Swamynathan, V.B.Sreenu, N.Pavan, S.Acharya and H.A.Nagarajaram** (2005) Frontiers in Bioinformatics Research: The Biodiversity Issues "Biodiversity : Status and Prospects" Editors: Pramod Tandon, Manju Sharma and Renu Swarup, Narosa Publishing House, New Delhi.
3. Buddhaditta Bose, Gyan Rajkumar, M. Narendar Pavan, A RadhaRama Devi, H.A. Nagarajaram** (2004) NBSdb: New Born Screening Database Indian Journal of Medical Informatics online.
4. G Ranjit Kumar, M Narendar Pavan, B. Bose, S Swaminathan, Geetha Thanu, P Prashanthi, B Phani Prasad, V B Sreenu, M Sridhar Achary and H A Nagarajaram** (2003) EMBnet India Node (EIN) at the Centre for DNA Fingerprinting and Diagnostics: Serving the Indian sub-continent in Bioinformatics Bioinformatics India 1 2:67-77.
5. H.A.Nagarajaram** and S.E.Hasnain** (2003) Current Status of Post-Genomics Computational Biology in "Computing and Information Sciences : Recent Trends" Editor: J.C.Misra, Narosa Publishing House, New Delhi.

Edited Books :

• Advanced Computing and Communication Technologies Proceedings of the 9th ICACCT, 2015 Choudhary, R.K., Mandal, J.K., Auluck, N., Nagarajaram, H.A. (Eds.) Advances in Intelligent Systems and Computing,  Springer (2016)