Trivedi, Rakesh and Nagarajaram, H.A. (2020) Substitution Scoring Matrices for Proteins ‐ An Overview. Protein Science, 29 (11). pp. 2150-2163. ISSN 0961-8368

Parapatla, H. and Gudla, R. and Konduru, G.V. and Devadasu, E.R. and Nagarajaram, H.A. and Sritharan, M. and Subramanyam, R. and Siddavattam, D. (2020) Organophosphate hydrolase interacts with ferric-enterobactin and promotes iron uptake in association with TonB dependent transport system. Biochemical Journal, 477 (15). pp. 2821-2840. ISSN 0264-6021

Trivedi, Rakesh and Nagarajaram, H.A. (2019) Amino acid substitution scoring matrices specific to intrinsically disordered regions in proteins. Scientific Reports, 9. p. 16380. ISSN 2045-2322

Gudla, R. and Konduru, G.V. and Nagarajaram, H.A. and Siddavattam, D. (2019) Organophosphate hydrolase interacts with Ton components and is targeted to the membrane only in the presence of the ExbB/ExbD complex. FEBS Letters, 593 (6). pp. 581-593. ISSN 0014-5793

Taware, R. and Taunk, K. and Pereira, J.A.M. and Shirolkar, A. and Soneji, D. and Câmara, J.S. and Nagarajaram, H.A. and Rapole, S. (2018) Volatilomic insight of head and neck cancer via the effects observed on saliva metabolites. Scientific Reports, 8 (1). p. 17725. ISSN 2045-2322

Taunk, K. and Taware, R. and More, T.H. and Porto-Figueira, P. and Pereira, J.A.M. and Mohapatra, R. and Soneji, D. and Câmara, J.S. and Nagarajaram, H.A. and Rapole, S. (2018) A non-invasive approach to explore the discriminatory potential of the urinary volatilome of invasive ductal carcinoma of the breast. RSC Advances, 8 (44). pp. 25040-25050. ISSN 2046-2069

Cavaco, C. and Pereira, J.A.M. and Taunk, K. and Taware, R. and Rapole, S. and Nagarajaram, H.A. and Câmara, J.S. (2018) Screening of salivary volatiles for putative breast cancer discrimination: an exploratory study involving geographically distant populations. Analytical and Bioanalytical Chemistry, 410 (18). pp. 4459-4468. ISSN 1618-2642

Taware, R. and Taunk, K. and Pereira, J.A.M. and Dhakne, R. and Kannan, N. and Soneji, D. and Camara, J.S. and Nagarajaram, H.A. and Srikanth, R. (2017) Investigation of urinary volatomic alterations in head and neck cancer: a non-invasive approach towards diagnosis and prognosis. Metabolomics, 13. p. 111. ISSN 1573-3882

Kumar, Parveen and Prathyusha, M. and Chowdary, K.V.S.R. and Shah, V.J. and Shinde, S.R. and Kolli, N.R. and Rachita, H.R. and Nagarajaram, H.A. and Subba Reddy, Maddika (2017) A human tyrosine phosphatase interactome mapped by proteomic profiling. Journal of Proteome Research, 16 (8). pp. 2789-2801. ISSN 1535-3893

Chaudhary, A.K. and Mohapatra, R. and Nagarajaram, H.A. and Ranganath, P. and Dalal, Ashwin and Dutta, A. and Danda, S. and Girisha, K.M. and Bashyam, M.D. (2017) The novelEDARp.L397H missense mutation causes autosomal dominant hypohidrotic ectodermal dysplasia. Journal of the European Academy of Dermatology and Venereology, 31 (1). e17-e20. ISSN 0926-9959

Kiran, M. and Nagarajaram, H.A. (2016) Interaction and localization diversities of global and local hubs in human protein–protein interaction networks. Molecular BioSystems, 12 (9). pp. 2875-2882. ISSN 1742-206X

Radha Rama Devi, A. and Ramesh, V.A. and Nagarajaram, H.A. and Satish, S.P.S. and Jayanthi, U. and Lingappa, L. (2016) Spectrum of mutations in Glutaryl-CoA dehydrogenase gene in glutaric aciduria type I – Study from South India. Brain and Development, 38 (1). pp. 54-60. ISSN 0387-7604

Uttarilli, Anusha and Ranganath, P. and Jain, S.J.M.N. and Krishnaprasad, C. and Sinha, A. and Verma, I.C. and Phadke, S.R. and Puri, R.D. and Danda, S. and Muranjan, M. and Jevalikar, G. and Nagarajaram, H.A. and Dalal, Ashwin (2015) Novel mutations of the arylsulphatase B (ARSB) gene in Indian patients with mucopolysaccharidosis type VI. Indian Journal of Medical Research, 142 (4). pp. 414-425. ISSN 0971-5916

Bidchol, A.M. and Dalal, Ashwin and Trivedi, R. and Shukla, A. and Nampoothiri, S. and Sankar, V.H. and Danda, S. and Gupta, N. and Kabra, M. and Hebbar, S.A. and Bhat, R.Y. and Matta, D. and Ekbote, A.V. and Puri, R.D. and Phadke, S.R. and Gowrishankar, K. and Aggarwal, Shagun and Ranganath, P. and Sharda, S. and Kamate, M. and Datar, C.A. and Bhat, K. and Kamath, N. and Shah, H. and Krishna, S. and Gopinath, P.M. and Verma, I.C. and Nagarajaram, H.A. and Satyamoorthy, K. and Girisha, K.M. (2015) Recurrent and novel GLB1 mutations in India. Gene, 567 (2). pp. 173-181. ISSN 0378-1119

Rachita, H.R. and Nagarajaram, H.A. (2015) Molecular principles of human virus protein-protein interactions. Bioinformatics (Oxford, England), 31 (7). pp. 1025-33. ISSN 1367-4811

Pereira, J. and Porto-Figueira, P. and Cavaco, C. and Taunk, K. and Rapole, S. and Dhakne, R. and Nagarajaram, H.A. and Câmara, J.S. (2015) Breath analysis as a potential and non-invasive frontier in disease diagnosis: an overview. Metabolites, 5 (1). pp. 3-55. ISSN 2218-1989

Bashyam, M.D. and Chaudhary, A.K. and Kiran, M. and Reddy, V. and Nagarajaram, H.A. and Dalal, Ashwin and Bashyam, L. and Sun, D. and Gupta, A. and Gupta, N. and Kabra, M. and Puri, R.D. and Radha Rama Devi, A. and Kapoor, S. and Danda, S. (2014) Molecular analyses of novel ASAH1 mutations causing Farber lipogranulomatosis: analyses of exonic splicing enhancer inactivating mutation. Clinical Genetics, 86 (6). pp. 530-538. ISSN 1399-0004

Patil, S.J. and Rai, G.K. and Bhat, V. and Ramesh, V.A. and Nagarajaram, H.A. and Matalia, J. and Phadke, S.R. (2014) Distal Arthrogryposis Type 5D With a Novel ECEL1 Gene Mutation. American Journal of Medical Genetics Part A, 164A (11). pp. 2857-2862. ISSN 1552-4833

Bidchol, A.M. and Dalal, Ashwin and Shah, H. and Suryanarayana, S. and Nampoothiri, S. and Kabra, M. and Gupta, N. and Danda, S. and Gowrishankar, K. and Phadke, S.R. and Kapoor, S. and Kamate, M. and Verma, I.C. and Puri, R.D. and Sankar, V.H. and Radha Rama Devi, A. and Patil, S.J. and Ranganath, P. and Jain, S.J.M.N. and Agarwal, Meenal and Singh, Ankur and Mishra, P. and Tamhankar, P.M. and Gopinath, P.M. and Nagarajaram, H.A. and Satyamoorthy, K. and Girisha, K.M. (2014) GALNS Mutations in Indian Patients With Mucopolysaccharidosis IVA. American Journal of Medical Genetics Part A, 164A (11). pp. 2793-2801. ISSN 1552-4833

Sinha, A. and Nagarajaram, H.A. (2014) Nodes occupying central positions in human tissue specific PPI networks are enriched with many splice variants. Proteomics, 14 (20). pp. 2242-2248. ISSN 1615-9853

Rachita, H R. and Nagarajaram, H.A. (2014) Viral proteins that bridge unconnected proteins and components in the human PPI network. Molecular BioSystems, 10 (9). pp. 2448-2458. ISSN 1742-206X

Bashyam, M.D. and Chaudhary, A.K. and Kiran, M. and Nagarajaram, H.A. and Radha Rama Devi, A. and Ranganath, P. and Dalal, Ashwin and Bashyam, L. and Gupta, N. and Kabra, M. and Muranjan, M. and Puri, R.D. and Verma, I.C. and Nampoothiri, S. and Kadandale, J.S. (2014) Splice, insertion-deletion and nonsense mutations that perturb the phenylalanine hydroxylase transcript cause phenylketonuria in India. Journal of Cellular Biochemistry, 115 (3). pp. 566-74. ISSN 1097-4644

Mudunuri, S.B. and Patnana, S. and Nagarajaram, H.A. (2014) MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes. Database : the Journal of Biological Databases and Curation, 2014. bau005. ISSN 1758-0463

Kiran, M. and Nagarajaram, H.A. (2013) Global versus Local Hubs in Human Protein–Protein Interaction Network. Journal of Proteome Research, 12 (12). pp. 5436-5446. ISSN 1535-3893

Sinha, A. and Nagarajaram, H.A. (2013) Effect of Alternative Splicing on the Degree Centrality of Nodes in Protein–Protein Interaction Networks ofHomo sapiens. Journal of Proteome Research, 12 (4). pp. 1980-1988. ISSN 1535-3893

Acharya, V. and Nagarajaram, H.A. (2013) Response to: Statistical Analysis of Missense Mutation Classifiers. Human Mutation, 34 (2). p. 407. ISSN 1059-7794

Bashyam, M.D. and Chaudhary, A.K. and Sinha, M. and Nagarajaram, H.A. and Radha Rama Devi, A. and Bashyam, L. and Reddy, E.C. and Dalal, Ashwin (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 Biochemistry, 113 (10). pp. 3122-3132. ISSN 0730-2312

Kumar, P. and Nagarajaram, H.A. (2012) A Study on Mutational Dynamics of Simple Sequence Repeats in Relation to Mismatch Repair System in Prokaryotic Genomes. Journal of Molecular Evolution, 74 (3-4). pp. 127-139. ISSN 0022-2844

Bashyam, M.D. and Chaudhary, A.K. and Reddy, E.C. and Reddy, V. and Acharya, V. and Nagarajaram, H.A. and Radha Rama Devi, A. and Bashyam, L. and Dalal, Ashwin and Gupta, N. and Kabra, M. and Agarwal, Meenal and Phadke, S.R. and Tainwala, R. and Kumar, R. and Hariharan, S.V. (2012) A founder ectodysplasin A receptor (EDAR) mutation results in a high frequency of the autosomal recessive form of hypohidrotic ectodermal dysplasia in India. British Journal of Dermatology, 166 (4). pp. 819-829. ISSN 0007-0963

Acharya, V. and Nagarajaram, H.A. (2012) Hansa: An automated method for discriminating disease and neutral human nsSNPs. Human Mutation, 33 (2). pp. 332-337. ISSN 1059-7794

Bashyam, M.D. and Purushotham, G. and Chaudhary, A.K. and Rao, K.M. and Acharya, V. and Mohammad, T.A.S. and Nagarajaram, H.A. and Hariram, V. and Narasimhan, C. (2012) A low prevalence of MYH7/MYBPC3 mutations among Familial Hypertrophic Cardiomyopathy patients in India. Molecular and Cellular Biochemistry, 360 (1-2). pp. 373-382. ISSN 0300-8177

Mudunuri, S.B. and Nagarajaram, H.A. and Mishra, P. (2012) Distributional analysis and motif frequencies of compound microsatellite repeats in viral genomes. In: Proceedings of IEEE International Conference on Computing, Electronics & Electrical Technologies (ICCEET)., 21-22 March 2012 , Kumaracoil, India. ISBN: 978-1-4673-0211-1.

Mudunuri, S.B. and Nagarajaram, H.A. and Mishra, P. (2012) In silico survey of distribution and frequency of imperfect microsatellite repeats in viral genomes. In: International Conference on Data Science & Engineering (ICDSE), 18-20 July 2012 , Cochin, India. ISBN: 978-1-4673-2148-8 (pages 31-38).

Mohammad, T.A.S. and Nagarajaram, H.A. (2011) SVM-based method for protein structural class prediction using secondary structural content and structural information of amino acids. Journal of Bioinformatics and Computational Biology, 9 (4). pp. 489-502. ISSN 0219-7200

Kumar, P. and Chaitanya, P.S. and Nagarajaram, H.A. (2011) PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes. Nucleic Acids Research, 39 (Databa). D601-D605. ISSN 0305-1048

Mohammad, T.A.S. and Nagarajaram, H.A. (2011) A hierarchical approach to protein fold prediction. Journal of Integrative Bioinformatics, 8 (1). p. 185. ISSN 1613-4516

Mudunuri, S.B. and Kumar, P. and Appa Rao, A. and Pallamsetty, S. and Nagarajaram, H.A. (2010) G-IMEx: A comprehensive software tool for detection of microsatellites from genome sequences. Bioinformation, 5 (5). pp. 221-3. ISSN 0973-2063

Mudunuri, S.B. and Appa Rao, A. and Pallamsetty, S. and Nagarajaram, H.A. (2010) Comparative analysis of microsatellite detecting software: a significant variation in results and influence of parameters. In: International Symposium on Biocomputing , 15-17 Feb 2010, Kerala, India.

Purushotham, G. and Madhumohan, K. and Anwaruddin, M. and Nagarajaram, H.A. and Hariram, V. and Narasimhan, C. and Bashyam, M.D. (2010) The MYH7 p.R787H mutation causes hypertrophic cardiomyopathy in two unrelated families. Experimental and clinical cardiology, 15 (1). e1-4. ISSN 1918-1515

Mudunuri, S.B. and Appa Rao, A. and Pallamsetty, S. and Mishra, P. and Nagarajaram, H.A. (2009) VMD: Viral Microsatellite Database-A Comprehensive Resource for all Viral Microsatellites. Journal of Computer Science & Systems Biology, 02 (06). pp. 283-286. ISSN 0974-7230

Korupolu, R.V. and Achary, M.S. and Aneesa, F. and Sathish, K. and Wasia, R. and Sairam, M. and Nagarajaram, H.A. and Singh, S.S. (2009) Profilin oligomerization and its effect on poly (l-proline) binding and phosphorylation. International Journal of Biological Macromolecules, 45 (3). pp. 265-273. ISSN 0141-8130

Achary, M.S. and Nagarajaram, H.A. (2009) Effects of Disease Causing Mutations on the Essential Motions in Proteins. Journal of Biomolecular Structure and Dynamics, 26 (5). pp. 609-623. ISSN 0739-1102

Achary, M.S. and Nagarajaram, H.A. (2008) Comparative docking studies of CYP1b1 and its PCG-associated mutant forms. Journal of Biosciences, 33 (5). pp. 699-713. ISSN 0250-5991

Shamim, M.T.A. and Anwaruddin, M. and Nagarajaram, H.A. (2007) Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs. Bioinformatics, 23 (24). pp. 3320-3327. ISSN 1367-4803

Mudunuri, S.B. and Nagarajaram, H.A. (2007) IMEx: Imperfect Microsatellite Extractor. Bioinformatics, 23 (10). pp. 1181-1187. ISSN 1367-4803

Vidyasagar, M. and Hasnain, S.E. and Mande, S.C. and Nagarajaram, H.A. and Ranjan, Akash and Acharya, M.S. and Anwaruddin, M. and Arun, S.K. and Gyanrajkumar, and Kumar, D. and Priya, S. and Ranjan, S. and Reddi, B.R. and Seshadri, J. and Sravan Kumar, P. and Swaminathan, S. and Uma Devi, P. and Vindal, V. and Vijaykrishnan, S. (2007) BioSuite: A comprehensive bioinformatics software package (A unique industry-academia collaboration). Current Science, 92 (1). pp. 29-38. ISSN 0011-3891

Sreenu , V.B. and Kumar, P. and Nagaraju, J. and Nagarajaram, H.A. (2007) Simple sequence repeats in mycobacterial genomes. Journal of Biosciences, 32 (1). pp. 3-15. ISSN 0250-5991

Achary, M.S. and Reddy, A.B.M. and Chakrabarti, S. and Panicker, S.G. and Mandal, A.K. and Ahmed, N. and Balasubramanian, D. and Hasnain, S.E. and Nagarajaram, H.A. (2006) Disease-Causing Mutations in Proteins: Structural Analysis of the CYP1b1 Mutations Causing Primary Congenital Glaucoma in Humans. Biophysical Journal, 91 (12). pp. 4329-4339. ISSN 0006-3495

Sreenu, V.B. and Kumar, P. and Nagaraju, J. and Nagarajaram, H.A. (2006) Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: Implications on genome evolution and plasticity. BMC Genomics, 7 (1). p. 78. ISSN 1471-2164

Cheeran, A. and Suganthan, R.B. and Swapna, G. and Bandey, I. and Achary, M.S. and Nagarajaram, H.A. and Sen, Ranjan (2005) Escherichia coli RNA Polymerase Mutations Located Near the Upstream Edge of an RNA:DNA Hybrid and the Beginning of the RNA-exit Channel are Defective for Transcription Antitermination by the N Protein from Lambdoid Phage H-19B. Journal of Molecular Biology, 352 (1). pp. 28-43. ISSN 0022-2836

Prasad, M.D. and Muthulakshmi, M. and Arunkumar, K.P. and Madhu, M. and Sreenu, V.B. and Pavithra, V. and Bose, B. and Nagarajaram, H.A. and Mita, K. and Shimada, T. and Nagaraju, J. (2005) SilkSatDb: a microsatellite database of the silkworm, Bombyx mori. Nucleic Acids Research, 33 (Supp 1). D403-D406. ISSN 1362-4962

Kamal, A. and Ramesh, G. and Srinivas, O. and Ramulu, P. and Laxman, N. and Rehana, T. and Deepak, M. and Achary, M.S. and Nagarajaram, H.A. (2004) Design, synthesis, and evaluation of mixed imine–amine pyrrolobenzodiazepine dimers with efficient DNA binding affinity and potent cytotoxicity. Bioorganic & Medicinal Chemistry, 12 (20). pp. 5427-5436. ISSN 0968-0896

Majeed, A.A. and Ahmed, N. and Rao, K.R. and Ghousunnissa, S. and Kauser, F. and Bose, B. and Nagarajaram, H.A. and Katoch, V.M. and Cousins, D.V. and Sechi, L.A. and Gilman, R.H. and Hasnain, S.E. (2004) AmpliBASE MTTM: a Mycobacterium tuberculosis diversity knowledgebase. Bioinformatics, 20 (6). pp. 989-992. ISSN 1367-4803

Sreenu, V.B. and Alevoor, V. and Nagaraju, J. and Nagarajaram, H.A. (2003) MICdb: database of prokaryotic microsatellites. Nucleic Acids Research, 31 (1). pp. 106-108. ISSN 1362-4962

Nagarajaram, H.A. and Hasnain, S.E. (2003) Current Status of Post-Genomics Computational Biology. In: Computing and Information Sciences: Recent Trends. Narosa Publihing House. ISBN 978-81-7319-491-7

Sreenu, V.B. and Ranjitkumar, G.K. and Swaminathan, S. and Priya, S. and Bose, B. and Pavan, M.N. and Thanu, G. and Nagaraju, J. and Nagarajaram, H.A. (2003) MICAS: a fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences. Applied Bioinformatics, 2 (3). pp. 165-168. ISSN 1175-5636

Eswar, N. and Nagarajaram, H.A. and Ramakrishnan, C. and Srinivasan, N. (2002) Influence of solvent molecules on the stereochemical code of glycyl residues in proteins. Proteins: Structure, Function, and Genetics, 49 (3). pp. 326-334. ISSN 0887-3585

Kamal, A. and Ramesh, G. and Laxman, N. and Ramulu, P. and Srinivas, O. and Neelima, K. and Kondapi, A.K. and Sreenu, V.B. and Nagarajaram, H.A. (2002) Design, Synthesis, and Evaluation of New Noncross-Linking Pyrrolobenzodiazepine Dimers with Efficient DNA Binding Ability and Potent Antitumor Activity. Journal of Medicinal Chemistry, 45 (21). pp. 4679-4688. ISSN 0022-2623

Panicker, S.G. and Reddy, A.B.M. and Mandal, A.K. and Ahmed, N. and Nagarajaram, H.A. and Hasnain, S.E. and Balasubramanian, D. (2002) Identification of novel mutations causing familial primary congenital glaucoma in Indian pedigrees. Investigative Ophthalmology & Visual Science, 43 (5). pp. 1358-66. ISSN 0146-0404