A. Polypeptides and Proteins 

1. Polypeptide models of Collagen. I. Solution properties of (Gly-Pro-Sar) and (Gly-Sar-Pro)n.
V. S. Ananthanaryanan, Samir K. Brahmachari, Rao, S. Rapaka and R. S. Bhatnagar. 
Biopolymers (1976) 15(4): 707 

2. Polypeptide models of Collagen, II. Solution properties of (Pro-Gly-Phe) n.
Samir K. Brahmachari, V.S. Ananthanaryanan, Rao, S. Rapaka and R.S. Bhatnager. 
Biopolymers (1978) 17(9): 2096 

3. Structural investigations on Poly-4-hydroxy-L-proline I.Theoretical studies.
M. Bansal, Samir K. Brahmachari and V. Sasisekharan. 
Macromolecules (1979) 12: 19 

4. Structural investigations on Poly-4-hydroxy-L-proline. II. Physico-chemical and X-ray studies.
Samir K. Brahmachari, M. Bansal, V.S.Ananthanaryanan, V. Sasisekharan. 
Macromolecules (1978) 12: 23 

5. Conformational criteria for the enzymatic hydroxylation of proline in collagen.
Samir K. Brahmachari and V.S.Ananthanaryanan. 
Curr. Sci.(1978) 47: 107 

6. b-turns in nascent procollagen are sites of po7st translational enzymatic hydroxylation of proline. Samir K. Brahmachari and V.S. Ananthanaryanan.
Proc. Natl. Acad, Sci. USA, (1979) 76: 5119 

7. Vacuum Ultraviolet Circular dichroism spectrum of b-turn in solution.
Samir K. Brahmachari, V.S.Ananthanaryanan, J. Brahms, S. Brahms, Rao, S. Rapaka 
and R.S. Bhatnagar. 
Biochem. Biophys. Res. Comm. (1979) 86: 605 

8. b-turn conformation of N-acetyl-Pro-Gly-Phe-OH in crystal and solution and its relevance to collagen.
V.S.Ananthanaryanan, Samir K. Brahmachari and M. Vijayan. 
Federation Proc. (1980) 39: 1788 

9. Crystal structure and solution studies on N-acetyle-Pro-Gly- Phe-OH. 
Samir K. Brahmachari, V.S.Ananthanaryanan, T.N. Bhat, V. Sudhakar, M. Vijayan, Rao, S. Rapaka and R.S. Bhatnagar. 
J.Amer. Chem. Soc. (1981) 103: 1703 

10. Proline containing b-turns in –peptides and proteins. I. Physico-chemical studies on N-acetyl- Pro-Gly-X-OH tri- peptides 
Samir K. Brahmachari, V.S.Ananthanaryanan, Rao, S. Rapaka and R.S.Bhatnagar. 
Biopolymers (1982) 21: 1208. 

11. Proline containing b-turns in peptides and proteins. II. Analysis of globular protein data. 
V.S.Ananthanaryanan, Samir K. Brahmachari and N.Pattabiraman. 
Arch. Biochem. Biophysics (1984) 232: 482 

B. DNA Structural Polymorphism and Chromatin Organisation 

12. Site and role of the N-terminal fragment of the nucleosomal core histonesin their bind to deoxyribonucleic acid as determined by vibrational spectroscopy. 
M. couppez, Santiere, Samir K. Brahmachari, J. Brahms, J. Liquier and E. Taillandier. 
Biochemistry (1980) 19: 3358 

13. B to Z transition in a DNA fibre: The question of handedness of the duplex. 
V. Sasiskharan and Samir K. Brahmachari. 
Curr. Sci. (1981) 50: 10 

14. Conformational flexibility of DNA: A theoretical formalism and a few practical applications. 
V.Sasisekharan, M. Bansal, Samir K. Brahmachari and G. Gupta. 
Biomolecular sterreodynamics, ed. R.H. Sarma, Adenine Press, N.Y. (1981) 1: 123 

15. Conformation of DNA in chromatin reconstituted from poly(dA-dT) and the cor histones. 
S. Brahms, Samir K. Brahmachari, N. Angelier and J.G.Brahms. 
Nucleic Acids Res. (1981) 9: 4879 

16. B to Z transition in DNA and its biological implications. 
Samir K.Brahmachari, Latha P. Kadalayil, K. Majumdar, and V.K.Parnaik 
Proceedings of INDO-FRG seminar, BARC, (1983) : 106 

17. Critical cation balance in B«Z transition; Role of Li+. 
N. Ramesh and Samir K. Brahmachari. 
FEBS lett. (1983) 164: 33 

18. Temperature dependent ZÞB transitions in Poly (dG-dC). 
Latha P. Kadalayil, K. Majumdar and Samir K. Brahmachari. 
Curr. Sci, (1983) 52: 907 

19. X-ray diffraction studies on Mycobacterium Smegmatis DNA. 
M. Rajagopalan, Samir K. Brahmachari, V. Sasisekharan and R. Srivastava 
Biopolymers (1983) 22(7): 1633 

20. Structural organization of the meotic prophase chromatin in the rat testis. 
Rao B.J., Samir K. Brahmachari and Rao M.R.S. 
J.Biol.Chem, (1983) 258:13478 

21. A novel structural transition in poly (dG-Me5dC) :Z«B«Z. 
Latha P.Kadalayil and Samir K. Brahmachari. 
FEBS lett. (1985) 182:315 

22. Left handed DNA in synthetic and topologically constrained form V DNA and its implications in protein recognition. 
Shouche,Y.S., Latha P.Kadalayil, Ramesh N., Majumder K., Mandyan V. 
and Samir K. Brahmachari. 
Proc. Int symp. Biomol. Struct Interactions,Suppl.J.Biosciences (1985) 8: 563 

23. Poly (dG-dC) in the Z-form inhibits E.Coli DNA polymerase I and AMV DNA polymerase activity. 
Samir K. Brahmachari, Ramesh N., M.R.Das and Veena K.Parnaik. 
Biochemistry Int. (1985) 11: 281 

24. B to Z transitions in DNA and their biological implications.
Latha P.Kadalayil and Samir K. Brahmachari. 
J.Scientific & Industrial Res. (1986) 45: 521 

25. Sequence dependence and role of 5'-phosphate in B to Z transition. 
Majumder K., Samir K. Brahmachari and V.Sasisekharan. 
FEBS lett. (1986) 198: 240 

26. Use of volatile buffer at ambient temperature:Versatile approach to the purification of self complementary synthetic deoxyribonucleotides by reverse phase high performance liquid chromatography. 
Majumder K.,Latha P.Kadalayil and Samir K.Brahmachari. 
J.Chromatography (1986) 355: 328. 

27. Recognition of B and Z forms of DNA by E.Coli DNA polymerase. 
Ramesh N.,Shouche Y.S. and Samir K. Brahmachari. 
J.Mol.Biol. (1986) 190: 635 

28. DNA structural variability as a factor in gene expression and evolution. 
Conrad M.,Samir K. Brahmachari and V. Sasisekharan. 
Biosystems (1986) 19: 123 

29. Sequences that adopt non B-form conformation in form V DNA as probed by enzymatic methylation. 
Samir K. Brahmachari, Shouche Y.S., Charles R. Cantor and M.McClelland. 
J.Mol.Biol. (1987) 193: 201 

30. Synthesis and purification of Oligodeoxyribonucleotides:A modified approach. 
Kumud Majumder, Latha P.Kadalayil and Samir K. Brahmachari. 
Curr. Sci. (1987) 56: 693 

31. Torsional stress, Unusual DNA structures; and Eukaryotic gene expression. 
C. R. Cantor, S. Bandopadhaya, Samir K. Brahmachari, C.F. Hui, M.McClelland, R. Morse and C. L. Smith. 
“Unusual DNA structure”; Ed. R.D. Wells and S.C. Harvey. Springer-Verlag, New York, (1988) 

32. Sequence specificity of Z-DNA formation in Oligonucleotides. 
Latha P.Kadalayil, Kumud Majumder, R. K. Mishra and Samir K. Brahmachari. 
Biochemistry Int. (1988) 17: 121 

33. Interruption of (CG)n sequences by GG, TG nad CA need not prevent B to Z transition in solution. 
R.K.Mishra, Latha P. Kadalayil and Samir K. Brahmachari. 
Nucleic Acids Res. (1988) 16: 4651 

34. Synthesis of novel polynucleotide: Potential R-L model.
R.K.Mishra and Samir K. Brahmachari. 
Curr. Sci. (1988) 57: 574 

35. Dynamic nature of B to Z transition: Role of DNA supercoiling and Z-DNA binding protein. 
N. Ramesh and Samir K. Brahmachari. 
Ind. J. Biochem. Biophys. Silver Jubilee issue (1988) 25: 542 

36. Sequence criteria for Z-DNA formation: Studies on poly d(ACGT). 
Kumud Majumder, Rakesh K. Mishra, Manju Bansal and Samir K. Brahmachari. 
Nucleic Acids Res. (1989) 17: 450 

37. Sequence specificity in supermine induced structural changes in CG-oligomers. 
Kumud Majumder and Samir K. Brahmachari. 
Biochemistry In., (1989) 18: 455 

38. Structural alteration from non-B to B-form could reflect Dnase I hypersensitivity. 
N.Ramesh and Samir K. Brahmachari. 
J.Biomol.Struc. Dynamics (1989) 6: 899 

39. Zintrons in rat alpha-Lactalbumin gene. 
G.Meera, N.Ramesh and Samir K. Brahmachari. 
FEBS lett (1989) 251: 245 

40. Preparation of Megabase DNA from adult insects and mammalian spleen for pulse field gel electrophoresis. 
Vani Brahmachari, R.Nagasuma and Samir K. Brahmachari. 
J. Genetics (1989) 68: 185 

41. Unusual DNA structures:Sequence requirements and role in transcriptional control. 
Samir K. Brahmachari, N. Ramesh,Yogesh S. Souche, Rakesh K. Mishra, Rajesh Bagga and G. Meera. 
Structures & Methods, Vol 2, Eds.R.H.Sarma & M.H. Sarma. Adenine press (1990) 

42. DNA duplex with a potential to change handedness after every half a turn.
Samir K. Brahmachari, Rakesh K.Mishra, Rajesh Bagga and N.Ramesh 
Nucleic Acids Res. (1989) 17: 7273 

43. Role of Environment in the Interaction of Nonintercalators with Z-DNA.
K.Ekambareswara Rao, N.Ramesh, D.Chaudhary, Samir K. Brahmachari and 
Journal of Biomolecular Structure & Dynamics (1989) 7: 335 

44. Probing of unusual DNA structures in topologically constrained from V DNA:Use of restriction enzyme as a structural probe. 
ShoucheY.S., N.Ramesh and Samir K. Brahmachari 
Nucleic Acids Res. (1990) 18: 267 

45. Supercoil induced unusual DNA structures as transcriptional block.
Rajesh Bagga, N.Ramesh and Samir K. Brahmachari 
Nucleic Acids Res. (1990) 18: 3363-9 

46. Z-DNA Binding Protein Mediated Stabilization of the Z-conformation.
Samir K. Brahmachari, Eugenia T.Paulus, N.Krishnamachary and N.Ramesh 
In Protein Structure-Function (1990), Ed.Zaidi, Abbasi & Smith,TWEL Publishers,135 

47. A novel approach to design cis-acting DNA structural elements for regulation of gene expression in vivo. 
P.S.Sarkar,R.Bagga,P.Balagurumoorthy and Samir K. Brahmachari 
Curr. Sci. (1991) 60: 586 

C. Repetitive DNA: Structure, Function, Genome Organisation and Variation 

48. Distribution of simple repetitive (TG/CA)n and (CT/AG)n sequences in human and rodent genome. 
Jalaj Tripathi and Samir K. Brahmachari 
Journal of Biomolecular Structure & Dynamics (1991) 9:387-97 

49. Synthetic gene design to investigate the role of cis-acting DNA structural elements in regulation of gene expression in vivo. 
Samir K. Brahmachari, P.S.Sarkar, P.Balagurumoorthy, P.Burma and R.Bagga 
Nucleic Acids Res., Symp. Series (1991) 24: 163 

50. Hairpin and parallel quartet structures for telomeric sequences. 
P.Balagurumoorthy, Samir K. Brahmachari, Debasis Mohanty, Manju Bansal and V.Sasisekharan 
Nucleic Acids Res. (1992) 20: 4061-7 

51. Intramolecular triplex potential sequence within a gene down regulates its expression in vivo. 
P.S.Sarkar and Samir K. Brahmachari 
Nucleic Acids Res (1992) 20: 5713-8 

52. Genome Analysis I: A new approach for visualization of sequence organization in genomes. 
P.K.Burma, Alok Raj, Jayant K.Deb and Samir K. Brahmachari 
Journal of Biosciences (1992) 17: 395 

53. Polypurine-polypyrimidine sequences adopt unwound structure in pBR322 from V DNA as probed by single-hit analysis of HpaII sites.
R.Bagga and Samir K. Brahmachari 
Journal of Biomolecular Structure & Dynamics (1993) 10: 879 

54. Chaos game representations of similarities and differences between genomic sequences. 
S.Baranidharan, B.Sankaranarayanan and Samir K. Brahmachari 
International Journal of Genome Research (1994) 1: 309 

55. Intramolecular DNA triple helix and regulation of gene expression. 
Samir K. Brahmachari and P.S.Sarkar 
Structural Biology: State of Art 1993, Vol 2, Eds. R.H.Sarma and M.H.Sarma, Adenine press (1994) 

56. CA/TG sequence at the 5' end of oligo a-tracts strongly modulates DNA curvature. 
Akhilesh K.Nagaich, D.Bhattacharya, Samir K. Brahmachari and Manju Bansal 
J.Biol.Chem (1994) 269: 7824 

57. Structure and Stability of Human Telomeric Sequence. 
P.Balagurumoorthy and Samir K. Brahmachari 
J. Biol. Chem (1994) 269: 21858-69 

58. Synthetic gene design for modulation of gene expression in vivo. 
Samir K. Brahmachari, Partha S.Sarkar, P.K.Burma, U.S.Shaligram and S.S.Pataskar 
Proc. of the Ranbaxy Sym. On Mol. Genetics and Gene therapy (1995): 85-97 

59. Functional significance of simple repetitive sequences in the genome. 
Samir K. Brahmachari, G.Meera,Partha S.Sarkar, P.Balagurumoorthy, J.Tripathi, S.Raghavan, U.S.Shaligram and S.S.Pataskar 
Electrophoresis (1995) 16: 1705-1714 

60. Analysis of CAG/CTG triplet repeats in the human genome: Implication in transcription factor gene regulation. 
Rachna Bhandari and Samir K. Brahmachari 
J. Biosci. (1995) 20: 613 

61. Intra and interloop interactions in the folded G quartet structure of Oxytricha telomeric 
P.Balagurumoorthy and Samir K. Brahmachari 
Ind.J.Biochem.Biophys. (1995) 32: 385 

62. Polypurine/polypyrimidine sequences as cis acting transcriptional regulators. 
Samir K. Brahmachari, Partha S.Sarkar, Sowmya Raghavan, Malthy Narayan and Amit K.Maiti 
Gene (1997) 190: 17 

63. Positional preferences of polupurine/polypyrimidine sequences in the genome of 
S.cerevisiae:Implications for cis-regulation of gene expression. 
Sowmya Raghavan, Pradeep K.Burma and Samir K. Brahmachari 
Journal of Molecular Evolution (1997) 45: 485-498 

64. Human genome studies and intellectual property rights: Whither national interest? 
T R Sivaramjani and Samir K. Brahmachari 
Current Science (1997) 72: 708 

65. International Collaboration in genetic research. 
S. Chatterjee, Samir K. Brahmachari, S Jain, P. Majumder and T Reich. 
Nature Genetics (1997) 15: 124 

66. Variation at the MJD locus in the major psychoses. 
Q.Saleem, M.Vijayakumar, M.Mulsuddi, N.Chowdhary, S.Jain and Samir K. Brahmachari 
Am.J.Med.Genet. (1998) 81(5): 440-442 

67. Correlation of Clinical Profile of Mytonic dystrophy with CTG repeats in Mtotonin Protein kinase gene. 
M.Gourie-Devi, J.Ray Chaydhari, Anisya Vasanth, Q.Saleem, Mousumi Mutsuddi, Meera Gopinath, P.S.Sarkar and Samir K. Brahmachari 
Ind.J.Med.Res. (1998) 107: 187-196 

68. Investigating the role of Trinucleotide repeats in schizophrenia and bipolar disorder. 
Quasar Saleem, Sanjeev Jain and Samir K. Brahmachari 
In the Proceedings of 5th Annual Symp., Ranbaxy Science Foundation. On Molecular Intervention in Disease (1998), 85-89 

69. Peptide models for inherited neurodegenerative disorders: conformation and aggregation properties of long polyglutamine peptides with and without interruptions 
Deepak Sharma, Sunita Sharma, Santosh Pasha and Samir K. Brahmachari 
FEBS. Lett. (1999) 456(1):181-185 

70 The multitude of ‘omics’ and ‘omes’: Evolution of scientific terms in molecular biology in the new millennium. 
Srinivasn Ramachandran, Debasis Dash, Samir K. Brahmachari 
Current Science, (1999) 77(7): 846-847 

71. Polypurine/polypyrimidine repeats in complete bacterial genomes: Preference for 
polypurine repeats in protein-coding regions (1999). 
Sowmya Raghawan, Ramesh Hariharan and Samir K. Brahmachari 
Gene (2000) 242: 275-283 

72. Association analysis of CAG repeats at the KCNN3 locus in Indian patients with Bipolar disorder and Schizophrenia. 
Quasar Saleem, V.S. Sreevidya, J. Sudhir, J. Vijaya Savithri, Y. Gowda, V. Benegal, Chandrika B. Rao, Partha P. Majumder, Anuranjan Anand, Samir K. Brahmachari and Sanjeev Jain 
Am.J.Med.Genet. (2000) 96, 744-748 

73. Molecular analysis of autosomal dominant hereditary ataxias in the Indian population: High frequency of SCA2 and evidence for a common founder mutation. 
Quasar Saleem, Shweta Choudhry, Mitali Mukherji, Leena Bashyam, M.V.Padma, Amber Chakravarthy, M.C.Maheshwari, Satish Jain and Samir K. Brahmachari 
Human Genetics (2000) 106: 179-187 

74. Association analysis of 5HT transporter gene in bipolar disorder in the Indian population. 
Q. Saleem, S. Ganesh, M. Vijaykumar, Y.C.J.Reddy., Samir K. Brahmachari, Sanjeev Jain 
Am. J. Med. Genet. (2000) 92(2): 170-172 

75. Probing the polyglutamine puzzle in neurological disorders. 
Samir K. Brahmachari , Deepak Sharma , Sharma S, Santosh Pasha, Sen S, Quasar Saleem Q 
FEBS Lett. (2000) 472(1): 167-168 

76. Association of CAG repeat Loci on Chromosome 22 with Schizophrenia and Bipolar Disorder.
Quasar saleem, Debasis Dash, Charu Gandhi, Anupam Kishore, Vivek Benegal, Tessi Sherrin, Odity Mukerjee, Sanjeev Jain and Samir K. Brahmachari
Mol. Psychiatry (2001) 6(6): 694-700 

77. Progressive Myoclonus Epilepsy [EPM1] repeat d(CCCCGCCCCGCG)n forms folded hairpin structures. 
Shashank S. Pataskar, Debasis Dash and Samir K. Brahmachari 
J. Biomol. Struct. Dynamics (2001) 19(2):293-305 

78. Intramolecular I-motif structure at acidic pH for progressive Myoclonus Epilepsy [EPM 1] repeat d (CCCCGCCCCGCG)n.
Shashank S. Pataskar, Debasis dash and Samir K. Brahmachari 
J. Biomol. Struct. Dynamics (2001) 19(2):307-313 

79. The polyglutamine motif is highly conserved at the clock locus in various organisms and is not polymorphic in humans. 
Quasar Saleem, Anuranjan Anand, Sanjeev Jain and Samir K. Brahmachari 
Human Genetics (2001) 109(2): 136-142 

80. CAG repeat instability at SCA2 Locus: anchoring CAA interuptions and linked single nucleotide polymorphism. 
S. Choudhry, M. Mukerji, A. K. Srivastava, S. Jain, S. K. Brahmachari 
Hum. Mol. Genet. (2001) 10(21):2437-2446 

81. Molecular and Clinical Correlation in five Indian families with Spinocerelellar Ataxia 12. 
Achal K. Srivastava, Shweta Choudhry, Musuwadi S. Gopinath, Sanghamitra Roy, Manjari Tripathi, Samir K. Brahmachari, and Satish Jain 
Annals of Neurology (2001) 50 (6) : 786-800 

82. Poly purine.pyrimidine sequences upstream of the beta-galactosidase gene affect gene 
expression in Saccharomyces cerevisiae. 
Maiti AK, Brahmachari SK 
BMC Mol Biol (2001) 2(1):11 

83. A clinical study of patients with genetically confirmed Huntington's disease from India. 
Murgod UA, Saleem Q, Anand A, Brahmachari SK, Jain S, Muthane UB 
J Neurol Sci (2001) 15;190(1-2):73-8 

84. Study of the Single Nucleotide Polymorphism (SNP) at the palindromic sequence of 
Hypersensitive Site (HS)4 of the human ß -globin Locus Control region (LCR) in Indian 
Ritushree Kukreti, Chandrika B-Rao, Swapan Kr Das, Madhusnata De, Geeta Talukder, Flavian Vaz, I. C. Verma, Samir K. Brahmachari 
Am. J. Hemat. (2001) 69:77-79 

85. ACE insertion allele in relation to high altitude adaptation. 
M. A. Qadar Pasha, AP Khan, Ratan Kumar, SK Grover, T Norboo, KK Srivastava, W. Selvamurthy, SK Brahmachari
Annals of Human Genetics (2001): 65: 531-536 

86. Expanding colonies and expanding repeats. 
Quasar Saleem, Uday Murgod, Uday Muthane, Anuranjan Anand, Inder C Verma, 
Samir K. Brahmachari, Sanjeev Jain. 
Lancet (2002) 9; 359(9309): 895-6 

87. Functional Genomics & DNA chips. 
Samir K. Brahmachari 
Appl Biochem Biotech (2001) 96/1-3: 9-12 

88. Genome-wide expression profile of RNA polymerase II subunit mutant of yeast using microarray technology.
Beena Pillai, Samir K. Brahmachari and PP. Sadhale
Current Science, (2001) 81,5, 574-578 

89. Angiotensin converting enzyme I/D polymorphism in ethnically different populations of India. 
M A. Qadar Pasha, AP Khan, Ratan Kumar, SK Grover, KK Srivastava, W. Selvamurthy, SK Brahmachari 
J. Biosci. (2002) 27: 67-70 

90. Molecular analysis of Huntingtons disease and linked polymorphisms in the Indian population. 
Q. Saleem, S.Roy, U.Murgood, R.Saxeena, I.C. Verma, A.Anand, U.Muthane, S.Jain, S.Jain, S.K.Brahmachari 
Acta Neurol Scand. 2003 Oct; 108(4): 281-286 

91. Whole Genome Expression Profiles of Yeast RNA Polymerase II Core Subunit, Rpb4, in Stress and Nonstress Conditions. 
Pillai B, Verma J, Abraham A, Francis P, Kumar Y, Tatu U, Brahmachari SK, Sadhale PP. 
J. Biol Chem. (2003) 278(5): 3339-46 

92. A novel complexity measure for comparative analysis of protein sequences from complete genomes. 
Nandi T, Dash D, Ghai R, Rao CB, Kannan K, Brahmachari SK, Ramakrishnan C, Ramachandran
J. Biomol Struct Dyn. (2003) 20(5): 657-68 

93. Role of histidine interruption in mitigating the pathological effects of long polyglutamine stretches in SCA1: A molecular approach. Sen S., Dash D., Pasha S., and Brahmachari SK 
Protein Science (2003) 12(05): 953-962 

94. Non-random distribution of Alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22. 
Deepak Grover, Partha P. Majumder , Chandrika B. Rao, Samir K. Brahmachari , Mitali Mukerji
Molecular Biology and Evolution (2003) 20(9): 1420-4 

95. (TG:CA)(n) Repeats in Human Housekeeping Genes. 
Sharma VK, Rao CB, Sharma A, Brahmachari SK, Ramachandran S. 
J Biomol Struct Dyn. (2003) 21(2):303-10 

96. Arterial oxygen saturation under hypoxic environment of high altitude associates with routine physical activities of natives. 
M. A. Qadar Pasha, K. S. Kocherlakota, A. P. Khan, T. Norboo, S. K. Grover, M. A. Baig, W. Selvamurthy and S. K. Brahmachari 
Current Science (2003) 85(4):502-506 

97. Association of high-altitude systemic hypertension with the deletion allele-of the angiotensin- converting enzyme (ACE) gene. 
Kumar R, Qadar Pasha MA, Khan AP, Gupta V, Grover SK, Norboo T, Srivastava KK, Selvamurthy W, Brahmachari SK 
Int J Biometeorol (2003) 48(1):10-14 

98. Hairpin-duplex equilibrium reflected in the A-->B transition in an undecamer quasi-palindrome present in the locus control region of the human beta-globin gene cluster. 
Kaushik M, Kukreti R, Grover D, Brahmachari SK, Kukreti S. 
Nucleic Acids Res. (2003) 31(23):6904-15 

99. Recognition and analysis of protein coding genes in severe acute respiratory syndrome associated coronavirus. 
Sharma R, Maheshwari JK, Prakash T, Dash D, Brahmachari SK. 
Bioinformatics (2004) 20(7): 1074-80 

100. Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. 
Grover D, Mukerji M, Bhatnagar P, Kannan K, Brahmachari SK. 
Bioinformatics (2004) 20(6): 813-17 

101. A nonsense mutation in the synaptogyrin 1 gene in a family with schizophrenia. 
Verma R, Chauhan C, Saleem Q, Gandhi C, Jain S, Brahmachari SK. 
Biol Psychiatry (2004) 55(2):196-9 

102. CoPS: Comprehensive Peptide Signature Database. 
Tulika Prakash, Mamta Khandelwal, Dipayan Dasgupta, Debasis Dash*, Samir K. Brahmachari. 
Bioinformatics (2004) 20(16):2886-8 

103. Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependent mobile Alu elements. 
Ravi Shankar, Deepak Grover, Samir K. Brahmachari and Mitali Mukerji 
BMC Evolutionary Biology (2004) 4(1):37 

104. Clusters of proteins in archaeal and bacterial proteomes using compositional analysis. 
Nandi T, Brahmachari SK, Kannan K, Ramachandran S. 
In Silico Biol. (2004) 4(4):573-91 

105. Conformational Analysis of Invariant Peptide Sequences in Bacterial Genomes. 
Tulika Prakash, C. Ramakrishnan, Debasis Dash and Samir K. Brahmachari* 
J Mol Biol. (2005) 345(5):937-55 

106. Identification of a novel 45 repeat unstable allele associated with a disease phenotype at the MJD1/SCA3 locus. 
Padiath QS, Srivastava AK, Roy S, Jain S, Brahmachari SK. 
Am. J Med Genet B Neuropsychiatr Genet. (2005) 133(1):124-6 

107. Assessing natural variations in gene expression in humans by comparing with monozygotic twins using microarrays. 
Sharma A, Sharma VK, Horn-Saban S, Lancet D, Ramachandran S, Brahmachari SK. 
Physiol Genomics (2005) 21(1):117-23

108. Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes. 
Ganapathi M, Srivastava P, Das Sutar SK, Kumar K, Dasgupta D, Singh GP, Brahmachari V, Brahmachari SK. 
BMC Bioinformatics (2005) 6(1):126 

109. (TG/CA)n repeats in human gene families: abundance and selective patterns of distribution according to function and gene length. 
Sharma VK, Brahmachari SK, Ramachandran S.
BMC Genomics (2005) 6(1):83

110. Genomics and Functional Genomics 
Mitali Mukerji, Beena Pillai, Somdutta Sen and Samir K. Brahmachari. 
Textbook of Biotechnology (2005): 1349-1409, Eds. Dr. H.K.Das, Wiley Dreamtech Pvt. Ltd, Delhi. 

111. MLC1 Gene Is Associated with Schizophrenia and Bipolar Disorder in Southern India. 
R. Verma, M. Mukerji, D. Grover, C. B-Rao, S. Das, S. Kubendran, S. Jain, S.K. Brahmachari.
Biological Psychiatry (2005) 58(1):16-22

112. ALU-ring elements in the primate genomes. 
Grover D, Kannan K, Brahmachari SK, Mukerji M
Genetica (2005)124(2-3):273-89 

113. The Indian Genome Variation database (IGVdb): a project overview. 
The Indian Genome Variation Consortium (158 authors). 
S.K. Brahmachari 
Hum Genet. (2005) 118: 1–11 

114. SYNGR1 is associated with schizophrenia and bipolar disorder in southern India.
Verma R, Kubendran S, Das SK, Jain S, Brahmachari SK.
J Hum Genet. (2005) 50(12):635-40 

115. Association of DRD2 gene variant with schizophrenia. 
Ritushree Kukreti, Sudipta Tripathi, Pallav Bhatnagar, Simone Gupta, Chitra Chauhan, Shobhana Kubendran, Y.C. Janardhan Reddy, Sanjeev Jain, Samir K. Brahmachari. 
Neurosci Lett. (2006) 9;392(1-2):68-71 

116. Characterization of parallel and antiparallel G-tetraplex structures by vibrational spectroscopy. 
Guzman MR, Liquier J, Brahmachari SK, Taillandier E
Spectrochim Acta A Mol Biomol Spectrosc. (2006) 15;64(2):495-503 

117. Evidence of linkage and association on 18p11.2 for psychosis. 
Mukherjee O, Meera P, Ghosh S, Kubendran S, Kiran K, Manjunath KR, Subhash MN, Benegal V, Brahmachari SK, Majumder PP, Jain S.
Am J Med Genet B Neuropsychiatr Genet. (2006) 141B(8):868-73

118. Boolean Network Analysis of a Neurotransmitter Signaling Pathway. 
Simone Gupta; Siddharth S Bisht; Ritushree Kukreti; Sanjeev Jain; Samir K. Brahmachari. 
J Theor Biol. (2007) 244(3):463-9 

119. Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats. 
Sharma VK, Sharma A, Kumar N, Khandelwal M, Kumar Mandapati K, Horn-Saban S, Strichman- Almashanu L, Lancet D, Brahmachari SK, Ramachandran S
BMC Genomics (2006) 7:258 

120. A whole genome analysis of 5' regulatory regions of human genes for putative cis-acting modulators of nucleosome positioning. 
Ganapathi M, Singh GP, Sandhu KS, Brahmachari SK, Brahmachari V. 
Gene (2007) 391(1-2):242-51 

121. Recommendations of the 2006 Human Variome Project meeting
Appelbe W, Auerbach AD, Becker K, Bodmer W, Boone DJ, Boulyjenkov V, Brahmachari S, Brody L, Brookes A, Brown AF, Byers P, Cantu JM, Cassiman JJ, Claustres M, Concannon P, Cotton RG, den Dunnen JT, Flicek P, Gibbs R, Hall J, Hasler J, Katz M, Kwok PY, Laradi S, Lindblom A, Maglott D, Marsh S, Masimirembwa CM, Minoshima S, de Ramirez AM, Pagon R, Ramesar R, Ravine D, Richards S, Rimoin D, Ring HZ, Scriver CR, Sherry S, Shimizu N, Stein L, Tadmouri GO, Taylor G, Watson M.
Nature Genetics (2007) 39(4):433-6

122. Abundance of Dinucleotide Repeats and Gene Expression are Inversely Correlated: a role for gene function in addition to intron length. 
Sharma VK, Kumar N, Brahmachari SK, Ramachandran S.
Physiol Genomics (2007) 31(1):96-103

123. Structural assessment of glycyl mutationsin invariantly conserved motifs. 
Prakash T, Sandhu KS, Singh NK, Bhasin Y, Ramakrishnan C, Brahmachari SK.
Proteins (2007) 69(3):617-632

124. Serotonergic candidate genes and puerperal psychosis: an association study.
Kumar HB, Purushottam M, Kubendran S, Gayathri P, Mukherjee O, Murthy AR, Ghosh S, Chandra P, Reddy YC, Benegal V, Brahmachari SK, Jain S.
Psychiatr Genet. (2007) 17(5):253-260

125. A role for voltage-dependent anion channel Vdac1 in polyglutamine-mediated neuronal cell death. 
Ghosh T, Pandey N, Maitra A, Brahmachari SK, Pillai B.
PLoS ONE (2007) 2(11):e1170

126. Human Proteinpedia enables sharing of human protein data. 
Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A. 
Nat Biotechnol. (2008) 26(2):164-7 

127. Predicting protein homocysteinylation targets based on dihedral strain energy and pKa of cysteines.
Elayanambi Sundaramoorthy, Souvik Maiti, Samir K. Brahmachari, Shantanu Sengupta.
Proteins (2008) 71(3):1475-83

128. Genetic Landscape of the People of India: a Canvas for Disease Gene Exploration. 
The Indian Genome Variation Consortium (150 authors). 
Journal of Genetics (2008) 87(1): 3-20 

129. From diversity to delivery: the case of the Indian Genome Variation initiative. 
Hardy BJ, Séguin B, Singer PA, Mukerji M, Brahmachari SK, Daar AS 
Nat. Rev. Genet. (2008) 9(1):S9-14 

130. Evolutionary analysis of PHLPP1 gene in humans and non-human primates
Anbazhagan, Padmanabhan; Purushottam, Meera; Kumar, H B Kiran; Kubendran, Shobana; Mukherjee, Odity; Samir Kumar Brahmachari,; Jain, Sanjeev; Sowdhamini, Ramanathan 
Bioinformation (2008) 2(10): 471–474 

131. HGVbaseG2P: a central genetic association database. 
Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, Brookes AJ. 
Nucleic Acids Res. (2009) 37 (Database issue):D797-802 

132. Mapping Human Genetic Diversity in Asia. 
HUGO Pan- SNP Consortium, Abdulla MA, Ahmed I, Assawamakin A, Bhak J, Brahmachari SK, Calacal GC, Chaurasia A, Chen CH, Chen J, Chen YT, Chu J, Cutiongco-de la Paz EM, De Ungria MC, Delfin FC, Edo J, Fuchareon S, Ghang H, Gojobori T, Han J, Ho SF, Hoh BP, Huang W, Inoko H, Jha P, Jinam TA, Jin L, Jung J, Kangwanpong D, Kampuansai J, Kennedy GC, Khurana P, Kim HL, Kim K, Kim S, Kim WY, Kimm K, Kimura R, Koike T, Kulawonganunchai S, Kumar V, Lai PS, Lee JY, Lee S, Liu ET, Majumder PP, Mandapati KK, Marzuki S, Mitchell W, Mukerji M, Naritomi K, Ngamphiw C, Niikawa N, Nishida N, Oh B, Oh S, Ohashi J, Oka A, Ong R, Padilla CD, Palittapongarnpim P, Perdigon HB, Phipps ME, Png E, Sakaki Y, Salvador JM, Sandraling Y, Scaria V, Seielstad M, Sidek MR, Sinha A, Srikummool M, Sudoyo H, Sugano S, Suryadi H, Suzuki Y, Tabbada KA, Tan A, Tokunaga K, Tongsima S, Villamor LP, Wang E, Wang Y, Wang H, Wu JY, Xiao H, Xu S, Yang JO, Shugart YY, Yoo HS, Yuan W, Zhao G, Zilfalil BA; Indian Genome Variation Consortium. 
Science (2009) 326(5959): 1541-1545 

D. miRNA Mediated  Regulation

133. Targets for human encoded microRNAs in HIV genes. 
Manoj Hariharan, Vinod Scaria, Beena Pillai, Samir K. Brahmachari. 
Biochem Biophys Res Commun. (2005) 337(4):1214-1218 

134. Host-virus interaction : a new role for microRNAs.
Scaria V, Hariharan M, Maiti S, Pillai B, Brahmachari SK. 
Retrovirology (2006) 3(1):68 

135. microRNA: an Emerging Therapeutic
Scaria V, Hariharan M, Brahmachari SK, Maiti S, Pillai B. 
ChemMedChem. (2007) 2(6):789-792

136. Host–virus genome interactions: macro roles for microRNAs. 
Vinod Scaria, Manoj Hariharan, Beena Pillai, Souvik Maiti and Samir K. Brahmachari.
Cell Microbiol. (2007) 9(12):2784-94 

137. Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication 
Ahluwalia JK, Khan SZ, Soni K, Rawat P, Gupta A, Hariharan M, Scaria V, Lalwani M, Pillai B, Mitra D, Brahmachari SK. 
Retrovirology (2008) 5(1):117 

138. dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation 
Hariharan M, Scaria V, and Samir K Brahmachari 
BMC Bioinformatics (2009) 10:108 

139. Posttranscriptional regulation of interleukin-10 expression by hsa-miR-106a. 
Sharma A, Kumar M, Aich J, Hariharan M, Brahmachari SK, Agrawal A, Ghosh B. 
Proc Natl Acad Sci U S A. (2009) 106(14):5761-6 

140. Human miRNAs: an antiviral defense mechanism 
Soni, K; Ahluwalia, JK; Khan, SZ; Pillai, B; Mitra, D; and Samir K Brahmachari 
Retrovirology (2009) 6(2): 83 

141. A simple method for incorporating dynamic effects of intronic miRNA mediated regulation. 
Gokhale S, Hariharan M, Brahmachari SK, Gadgil C. 
Mol Biosyst. (2012), (8):2145-52 

Rakesh Dey, Kartik Soni, Shanmugam Saravanan, Pachamuthu Balakrishnan, Vikram Kumar, Jayaseelan Boobalan, Sunil Suhas Solomon, Vinod Scaria, Sunit Solomon,                        Samir K. Brahmachari & Beena Pillai.
Scientific Reports 6 (2016), Article number: 28279.

E. Pharmacogenomics and Translational Medicine

143. β2-adrenergic receptor polymorphisms and response to salbutamol among Indian asthmatics. 
Ritushree Kukreti, ­Pallav Bhatnagar, ­Chandrika B-Rao, ­Simone Gupta, ­ Babita Madan, Chinmoyee Das, ­Randeep Guleria, ­Amita Umesh Athavale, ­Samir Kumar Brahmachari & Balaram Ghosh­.
Pharmacogenomics (2005) 6(4): 399-410

144. Pharmacogenomics: a path to predictive medicine for schizophrenia. 
Simone Gupta​‌, ­ Sanjeev Jain​, ­Samir K Brahmachari & ­Ritushree Kukreti.­ 
Pharmacogenomics (2006) 7(1):31-47 

145. Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda 
Prasher B, Negi S, Aggarwal S, Mandal AK, Sethi TP, Deshmukh SR, Purohit SG, Sengupta S, Khanna S, Mohammad F, Garg G, Brahmachari SK; Indian Genome Variation Consortium, Mukerji M. 
J Transl Med. (2008) 6: 48

146. Genetic susceptibility to schizophrenia: role of dopaminergic pathway gene polymorphisms 
Gupta, M; Chauhan, C; Bhatnagar, P; Gupta, S; Grover, S; Singh, PK; Purushottam, M; Mukherjee, O; Jain, S; Samir K Brahmachari; Kukreti, R 
Pharmacogenomics (2009) 10(2): 277-291 

147. Association studies of catechol-O-methyltransferase (COMT) gene with schizophrenia and response to antipsychotic treatment
Gupta M, Bhatnagar P, Grover S, Kaur H, Baghel R, Bhasin Y, Chauhan C, Verma B, 
Manduva V, Mukherjee O, Purushottam M, Sharma A, Jain S, Brahmachari SK, Kukreti 
Pharmacogenomics (2009) 10(3):385-97 

148. Genetic profile of patients with epilepsy on first-line antiepileptic drugs and potential directions for personalized treatment 
Sandeep Grover , Mandaville Gourie-Devi , Ruchi Baghel , Sangeeta Sharma , Kiran Bala , Meena Gupta , Krishnamoorthy Narayanasamy , Binuja Varma, Meenal Gupta , Kavita Kaur , Puneet Talwar, Harpreet Kaur , Sudheer Giddaluru , Abhay Sharma , Samir K Brahmachari , Indian Genome Variation Consortium & Ritushree Kukreti 
Pharmacogenomics (2010) 11 (7): 927-941

149. Systems medicine and integrated care to combat chronic noncommunicable diseases
Bousquet J, Anto JM, Sterk PJ, Adcock IM, Chung KF, Roca J, Agusti A, Brightling C, Cambon-Thomsen A, Cesario A, Abdelhak S, Antonarakis SE, Avignon A, Ballabio A, Baraldi E, Baranov A, Bieber T, Bockaert J, Brahmachari SK, Brambilla C, Bringer J, Dauzat M, Ernberg I, Fabbri L, Froguel P, Galas D, Gojobori T, Hunter P, Jorgensen C, Kauffmann F, Kourilsky P, Kowalski ML, Lancet D, Pen CL, Mallet J, Mayosi B, Mercier J, Metspalu A, Nadeau JH, Ninot G, Noble D, Oztürk M, Palkonen S, Préfaut C, Rabe K, Renard E, Roberts RG, Samolinski B, Schünemann HJ, Simon HU, Soares MB, Superti-Furga G, Tegner J, Verjovski-Almeida S, Wellstead P, Wolkenhauer O, Wouters E, Balling R, Brookes AJ, Charron D, Pison C, Chen Z, Hood L, Auffray C. 
Genome Med. (2011) 6;3(7):43 

150. Introducing the Medical bioinformatics in Journal of Translational Medicine 
Brahmachari SK. 
J Transl Med. (2012); 10(1):202.

151. Integrating Health Care Delivery and Data Collection in Rural India Using a Rapidly Deployable, eHealth Center
Agrawal A, Bhattacharya J, Baranwal N, Bhatla S, Dube S, Sardana V, Gaur D R, Balazova D,
PLoS Med., (2013) 10(6): e1001468

Giri AK, Khan NM, Grover S, Kaur I, Basu A, Tandon N, Scaria V, Consortium I, Kukreti R, Brahmachari SK, Bharadwaj D.
Pharmacogenomics. 2014 Jul;15(10):1337-54. doi: 10.2217/pgs.14.88.

Michael Sagner, Amy McNeil, Pekka Puska, Charles Auffray, Nathan D. Price, Leroy Hood, Carl J. Lavie,  Ze-Guang Han, Zhu Chen, Samir Kumar Brahmachari, Bruce S. McEwen, Marcelo B. Soares, Rudi Balling, Elissa Epel, Ross Arena.
Progress in Cardiovascular Diseases (2016).

F. Affordable Drug Discovery

154. An Indian effort towards affordable drugs: "generic to designer drugs". 
Taneja B, Yadav J, Chakraborty TK, Brahmachari SK. 
Biotechnol J. (2009) 4(3):348-360 

155. Collaborative tools to accelerate neglected disease research: Open Source Drug Discovery model 
Bhardwaj A, Scaria V, Thomas Z, Adayikkoth S, Open Source Drug Discovery (OSDD) Consortium, And Samir K. Brahmachari 
Collaborative Computational Technologies for Biomedical Research (2011): 321-334, Eds. Sean Ekins, Maggie A. Z. Hupcey, Anthony Williams, John Wiley & Sons. 

156. Towards new business models for R&D for novel antibiotics
So AD, Gupta N, Brahmachari SK, Chopra I, Munos B, Nathan C, Outterson K, Paccaud JP, Payne DJ, Peeling RW, Spigelman M, Weigelt J. 
Drug Resist Updat. (2011) 14(2):88-94 

157. Open source drug discovery- A new paradigm of collaborative research in tuberculosis drug development
Bhardwaj A, Scaria V, Raghava GP, Lynn AM, Chandra N, Banerjee S, Raghunandanan MV, Pandey V, Taneja B, Yadav J, Dash D, Bhattacharya J, Misra A, Kumar A, Ramachandran S, Thomas Z, Brahmachari SK. 
Tuberculosis (Edinb). (2011) 91(5): 479-486. 

158. Structural annotation of Mycobacterium tuberculosis proteome. 
Anand P, Sankaran S, Mukherjee S, Yeturu K, Laskowski R, Bhardwaj A, Bhagavat R; OSDD Consortium, Brahmachari SK, Chandra N. 
PLoS One (2011) 6(10):e27044 

159. Crowd Sourcing a new paradigm for Interactome Driven Drug Target Identification in 
Mycobacterium tuberculosis 
Vashisht R, Mondal AK, Jain A, Shah A, Vishnoi P, Priyadarshini P, Bhattacharyya K, Rohira, H, Bhat H, Passi A, Mukherjee K, Sonal K, Kumar V, Arora A, Munusamy P, Subramanian A, Venkatachalam A, Gayathri S, Raj S, Chitra V, Verma K, Zaheer S, Balganesh J, Gurusamy M, Mohammed Razeeth, Ilamathi Raja, Thandapani M, Mevada V, Soni R, Rana S, Girish MR, Raghavan S, Sunil N, Kholia T, Patel R, Bhavnani V, Chiranjeevi L, Sengupta S, Singh PK, Atray N, Gandhi S, Avasthi S, Nisthar S, Anurag M, Sharma P, Hasija Y, Dash D, Sharma A, Scaria V, Thomas Z, OSDD Consortium, Chandra N, Brahmachari SK and Bhardwaj A 
PLoS One (2012), 7(7):e39808 

160. Software Platform for Metabolic Network Reconstruction of Mycobacterium tuberculosis.
Ghosh S, Matsuoka Y, Asai Y, Kitano H, Bhardwaj A, Scaria V, Vashisht R, Shah A, Mondal AK, Vishnoi P, Sonal K, Jain A, Priyadarshini P, Bhattacharyya K, Kumar V, Passi A, Sharma P, Brahmachari SK.
Systems Biology of Tuberculosis (2013) Eds: Johnjoe McFadden, Dany J.V. Beste, Andrzej M. Kierzek, Springer

Vashisht R, Bhardwaj A, Osdd Consortium, Brahmachari SK.
Mol Biosyst, (2013), 9 (7): 1584 – 1593

Rohit Vashisht, Ashwini G Bhat, Shreeram Kushwaha, Anshu Bhardwaj, OSDD Consortium, Samir K Brahmachari
J Transl Med. 2014; 12(1): 263. Published online 2014 October 11. doi: 10.1186/s12967-014-0263-5  

Rohit Vashisht and Samir K Brahmachari
Journal of Translational Medicine 2015, 13:83  

164. Designing non-toxic ligands against TB using data intensive genome level analysis                D. Kaur, S. K. Brahmachari
J. Biol. Struct. Dyn., 2015, 33(1), 128

165. Data Intensive Genome Level Analysis for Designing Non-Toxic Ligands against Drug            Resistant Mycobacterium tuberculosis                                                                                  Divneet Kaur, Rintu Kutum, Debashish Dash, &  Samir Brahmachari. (Submitted)

Sudheer Gupta, Kumardeep Chaudhary, Rahul Kumar, Ankur Gautam, Jagpreet Singh Nanda, Sandeep Kumar Dhanda, Samir Kumar Brahmachari & Gajendra P. S. Raghava               Scientific Reports(2016); 6,Article number: 23857.

167. A web-based resource for designing therapeutics against Ebola Virus                               Sandeep Kumar Dhanda, Kumardeep Chaudhary, Sudheer Gupta, Samir Kumar Brahmachari and Gajendra P. S. Raghava.
Scientific Reports(2016); 6,Article number: 24782.

G.   Innovation and Policy

Nisha Chandran and Samir K Brahmachari
Current Science; 25 October 2015, 109 (08)    

Nisha Chandran and Samir Kumar Brahmachari
Journal of Frugal Innovation 2015, 1:3

Manisha G. Singh, Nisha Chandran, Zakir Thomas, Dipankar Basu, Samir K.Brahmchari             Economic and Political Weekly 2016

 Nisha Chandran, Manisha G. Singh, Zakir Thomas, Dipankar Basu, Samir K. Brahmchari
Economic and Political Weekly 2016


Publications where Dr. Brahmachari is a lead “Indian Genome Variation Consortium” Author 

1. Allelic heterogeneity of molecular events in human coagulation factor IX in Asian Indians Mutation in brief #965 Online.
Mahajan A, Chavali S, Ghosh S, Kabra M, Chowdhury MR, Indian Genome Variation Consortium, Bharadwaj D. 
Hum Mutat. (2007) 28(5): 526 

2. Molecular diagnosis of Wilson disease using prevalent mutations and informative single-nucleotide polymorphism markers. Gupta A, Maulik M, Nasipuri P, Chattopadhyay I, Das SK, Gangopadhyay PK, Indian Genome Variation Consortium, Ray K. 
Clin Chem. (2007) 53(9): 1601-8 

3. Parkin polymorphisms: risk for Parkinson's disease in Indian population. Biswas A, Maulik M, Das SK, Indian Genome Variation Consortium, Ray K, Ray J. 
Clin Genet. (2007) 72(5): 484-6 

4. Evaluation of genetic markers linked to hemophilia A locus: an Indian experience. 
Saha A, Mukherjee S, Maulik M, Chandak GR, Indian Genome Variation Consortium, Ray K. 
Haematologica (2007) 92 (12): 1725-6 

5. Polymorphisms of TNF-enhancer and gene for FcgammaRIIa correlate with the severity of falciparum malaria in the ethnically diverse Indian population. Sinha S, Mishra SK, Sharma S, Patibandla PK, Mallick PK, Sharma SK, Mohanty S, Pati SS, Mishra SK, Ramteke BK, Bhatt R, Joshi H, Dash AP, Ahuja RC, Awasthi S, Indian Genome Variation Consortium, Venkatesh V, Habib S. 
Malar J. (2008) 7:13 

6. Leu432Val polymorphism in CYP1B1 as a susceptible factor towards predisposition to primary open-angle glaucoma.
Bhattacharjee A, Banerjee D, Mookherjee S, Acharya M, Banerjee A, Ray A, Sen A, Indian Genome Variation Consortium, Ray K.  
Mol Vis. (2008) 14: 841-50 

7. Variations in host genes encoding adhesion molecules and susceptibility to falciparum malaria in India. 
Sinha S, Qidwai T, Kanchan K, Anand P, Jha GN, Pati SS, Mohanty S, Mishra SK, Tyagi PK, Sharma SK, Indian Genome Variation Consortium, Venkatesh V, Habib S. 
Malar J. (2008) 7: 250 

8. Utilizing linkage disequilibrium information from Indian Genome Variation Database for mapping mutations: SCA12 case study. 
Bahl S, Ahmed I, Indian Genome Variation Consortium, Mukerji M. 
J Genet. (2009) 88(1): 55-60 

9. Genetic differentiation of populations residing in areas of high malaria endemicity in India. 
Sinha S, Arya V, Agarwal S, Indian Genome Variation Consortium, Habib S. 
J Genet. (2009) 88 (1): 77-80 

10. Single nucleotide polymorphisms in homocysteine metabolism pathway genes: association of CHDH A119C and MTHFR C677T with hyperhomocysteinemia. 
Kumar J, Garg G, Kumar A, Sundaramoorthy E, Sanapala KR, Ghosh S, Karthikeyan G, Ramakrishnan L, Indian Genome Variation Consortium, Sengupta S. 
Circ Cardiovasc Genet. (2009) 2(6): 599-606 

11. Evaluation of PINK1 variants in Indian Parkinson's disease patients. 
Biswas A, Sadhukhan T, Majumder S, Misra AK, Das SK, Indian Genome Variation Consortium IG, Ray K, Ray J. 
Parkinsonism Relat Disord. (2010) 16(3): 167-71 

12. Analysis of single nucleotide polymorphisms of PRNP gene in twenty-four ethnic groups of India. Sengupta M, Chakraborty A, 
Indian Genome Variation Consortium, Ray K. 
J Genet. (2010) 89(2): 247-51 

13. IGVBrowser--a genomic variation resource from diverse Indian populations. 
Narang A, Roy RD, Chaurasia A, Mukhopadhyay A, Mukerji M, Indian Genome Variation Consortium, Dash D. 
Database (Oxford). (2010): 2010:baq022 

14. EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda. 
Aggarwal S, Negi S, Jha P, Singh PK, Stobdan T, Pasha MA, Ghosh S, Agrawal A, Indian Genome Variation Consortium, Prasher B, Mukerji M. 
Proc Natl Acad Sci USA (2010) 107(44): 18961-6 

15. Molecular and functional studies of tyrosinase variants among Indian oculocutaneous albinism type 1 patients. 
Chaki M, Sengupta M, Mondal M, Bhattacharya A, Mallick S, Bhadra R, Indian Genome Variation Consortium, Ray K. 
J Invest Dermatol. (2011) 131(1): 260-2 

16. A set of five microsatellite markers linked to F8 gene can detect haemophilia A carriers across India. 
Saha A, Nayak S, Mani KR, Chandak GR, Indian Genome Variation Consortium, Ray K, Mukhopadhyay A. 
Haemophilia (2011) 17(5): e928-935 

17. Differential serum cytokine levels are associated with cytokine gene polymorphisms in north Indians with active pulmonary tuberculosis. 
Abhimanyu, Mangangcha IR, Jha P, Arora K, Mukerji M, Banavaliker JN, Indian Genome Variation Consortium, Brahmachari V, Bose M. 
Infect Genet Evol. (2011) 11(5): 1015-22 

18. Spectrum of large copy number variations in 26 diverse Indian populations: potential involvement in phenotypic diversity. 
Gautam P, Jha P, Kumar D, Tyagi S, Varma B, Dash D, Mukhopadhyay A, Indian Genome Variation Consortium, Mukerji M. 
Hum Genet. (2011) 131(1): 131-143 

19. Recent admixture in an Indian population of african ancestry.
Narang A, Jha P, Rawat V, Mukhopadhayay A, Dash D, Indian Genome Variation Consortium, Basu A, Mukerji M. 
Am J Hum Genet. (2011) 89(1): 111-20 

20. HLA Alleles and Amino-Acid Signatures of the Peptide-Binding Pockets of HLA Molecules in Vitiligo. 
Singh A, Sharma P, Kar HK, Sharma VK, Tembhre MK, Gupta S, Laddha NC, Dwivedi M, Begum R, The Indian Genome Variation Consortium, Gokhale RS, Rani R. 
J Invest Dermatol. (2011) 132(1): 124-134 

21. Diverse facets of COMT: from a plausible predictive marker to a potential drug target for schizophrenia.
Gupta M, Kaur H, Jajodia A, Jain S, Satyamoorthy K, Mukerji M, Thirthalli J; Indian Genome Variation Consortium, Kukreti R.
Curr Mol Med. (2011) 11(9):732-43. 

22. Deletion of the APOBEC3B gene strongly impacts susceptibility to falciparum malaria.
Jha P, Sinha S, Kanchan K, Qidwai T, Narang A, Singh PK, Pati SS, Mohanty S, Mishra SK, Sharma SK, Awasthi S, Venkatesh V, Jain S, Basu A, Xu S; Indian Genome Variation Consortium, Mukerji M, Habib S.
Infect Genet Evol. (2012) 12(1):142-8. 

23. Identification of close relatives in the HUGO Pan-Asian SNP database.
Yang X, Xu S; HUGO Pan-Asian SNP Consortium; Indian Genome Variation Consortium.
PLoS One. (2011) 6(12):e29502

24. Presence of strong association of the major histocompatibility complex (MHC) class I allele HLA-A*26:01 with idiopathic hypoparathyroidism.
Goswami R, Singh A, Gupta N; Indian Genome Variation Consortium, Rani R.
J Clin Endocrinol Metab. (2012) 97(9):E1820-4

25. Footprints of genetic susceptibility to pulmonary tuberculosis: cytokine gene variants in north Indians.
Abhimanyu, Bose M, Jha P; Indian Genome Variation Consortium.
Indian J Med Res. (2012) 135(5):763-70

26.  Complex patterns of genomic admixture within southern Africa. Petersen DC, Libiger O, Tindall EA, Hardie RA, Hannick LI, Glashoff RH, Mukerji M; Indian Genome Variation Consortium, Fernandez P, Haacke W, Schork NJ, Hayes VM.
PLoS Genet. (2013);9(3):e100330

27. LIG1 polymorphisms: the Indian scenario. Mitra AK, Singh A; Indian Genome Variation Consortium, Rath SK.
J Genet.  (2014); 93(2):459-69.

28. Extensive copy number variations in admixed Indian population of African ancestry: potential involvement in adaptation. Narang A, Jha P, Kumar D, Kutum R, Mondal AK; Indian Genome Variation Consortium, Dash D, Mukerji M.
Genome Biol Evol.(2014);6(12):3171-81.

29. Population diversity and adaptive evolution in keratinization genes: impact of environment shaping skin phenotypes. Gautam P, Chaurasia A, Bhattacharya A, Grover R; Indian Genome Variation ConsortiumMukerji M, Natarajan VT.                                           Mol Biol Evol. (2015); 32(3):555-73.

30. Combined genetic effects of EGLN1 and VWF modulate thrombotic outcome in hypoxia revealed by Ayurgenomics approach.Aggarwal S, Gheware A, Agrawal A, Ghosh S, Prasher B, Mukerji M; Indian Genome Variation Consortium.                                                             J Transl Med. (2015).

31. Polymorphisms in host genes encoding NOSII, C-reactive protein, and adhesion molecules thrombospondin and E-selectin are risk factors for Plasmodium falciparum malaria in India. Kanchan K, Pati SS, Mohanty S, Mishra SK, Sharma SK, Awasthi S; Indian Genome Variation Consortium, Venkatesh V, Habib S.                                                   Eur J Clin Microbiol Infect Dis. (2015);34(10):2029-39.

32. Genetic contribution of CYP1A1 variant on treatment outcome in epilepsy patients: a functional and interethnic perspective.Talwar P, Kanojia N, Mahendru S, Baghel R, Grover S, Arora G, Grewal GK, Parween S, Srivastava A, Singh M, Vig S, Kushwaha S, Sharma S, Bala K; Indian Genome Variation Consortium, Kukreti S, Kukreti R.                         Pharmacogenomics J. (2016).

Publications where Dr. Brahmachari is a lead “Open Source Drug Discovery Consortium” Author 

1. TBrowse: an integrative genomics map of Mycobacterium tuberculosis.
Bhardwaj A, Bhartiya D, Kumar N; Open Source Drug Discovery Consortium, Scaria V. 
Tuberculosis (Edinb). (2009) 89(5): 386-7 

2. Open Source Drug Discovery: A Collaborative Drug Discovery Model for Tuberculosis. 
Bhardwaj A, Scaria V, Patra D, Open Source Drug Discovery Consortium. 
Science and Culture. (2011) 77(1): 22-26 

3. Predictive models for anti-tubercular molecules using machine learning on high-throughput biological screening datasets. 
Periwal V, Rajappan JK; Open Source Drug Discovery Consortium, Jaleel AU, Scaria V. 
BMC Res Notes. (2011) 18(4): 504 

4. ccPDB: compilation and creation of data sets from Protein Data Bank. 
Singh H, Chauhan JS, Gromiha MM; Open Source Drug Discovery Consortium, Raghava GP. 
Nucleic Acids Res. (2012) 40(Database issue):D486-9 

5. Computational models for in-vitro anti-tubercular activity of molecules based on high-throughput chemical biology screening datasets. 
Periwal V, Kishtapuram S; Open Source Drug Discovery Consortium, Scaria V 
BMC Pharmacol. (2012) 31;12:1.

6. In-silico predictive mutagenicity model generation using supervised learning approaches. 
Seal A, Passi A, Jaleel UA; Open Source Drug Discovery Consortium, Wild DJ.
J Cheminform. (2012) 15;4(1):10. 

7. Computational analysis and predictive modeling of small molecule modulators of microRNA. 
Jamal S, Periwal V, Consortium O, Scaria V. 
J Cheminform. (2012) 4(1):16. 

8. Computational screening for new inhibitors of M. tuberculosis mycolyltransferases antigen 85 group of proteins as potential drug targets. 
Gahoi S, Mandal RS, Ivanisenko N, Shrivastava P, Jain S, Singh AK, Raghunandanan MV, Kanchan S, Taneja B, Mandal C, et al
J Biomol Struct Dyn. (2013) 31(1):30-43.

9. Enhanced ranking of PknB Inhibitors using data fusion methods. 
Seal A, Yogeeswari P, Sriram D, Consortium O, Wild DJ
J Cheminform. 2013 Jan 14;5(1):2. 

10. Predictive modeling of anti-malarial molecules inhibiting apicoplast formation. 
Jamal S, Periwal V; Open Source Drug Discovery Consortium, Scaria V. 
BMC Bioinformatics. (2013) 14(1):55. 

11. Designing of inhibitors against drug tolerant Mycobacterium tuberculosis (H37Rv). Singla D1, Tewari R, Kumar A, Raghava GP; Open Source Drug Discovery Consortium.                   Chem Cent J. (2013);7(1):49.

12. In silico approaches for designing highly effective cell penetrating peptides.Gautam , Chaudhary K, Kumar R, Sharma A, Kapoor P, Tyagi A; Open source drug discovery consortium, Raghava GP.                                                                                J Transl Med. (2013);11:74.

     13. Draft Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium tuberculosis East African Indian Strain OSDD271. Karuthedath Vellarikkal , Patowary A, Singh M, Periwal V, Singh AV, Singh PK, Garg P, Mohan Katoch V, Katoch K, Jangir PK, Sharma R; Open Source Drug Discovery Consortium, Chauhan DS, Scaria V, Sivasubbu S.                     Genome Announc.(2013);1(4).  

       14.  In silico approach for predicting toxicity of peptides and proteins. Gupta S, Kapoor P, Chaudhary K, Gautam A, Kumar R; Open Source Drug Discovery Consortium, Raghava GP.     PLoS One. (2013);8(9)

          15. Identification of B-cell epitopes in an antigen for inducing specific class of antibodies. Gupta S, Ansari HR, Gautam A; Open Source Drug Discovery Consortium, Raghava GP.                                                                                                             Biol Direct.(2013);8:27.

          16. Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate of the Ural Strain OSDD493. Karuthedath Vellarikkal S, Vir Singh A, Kumar Singh P, Garg P, Mohan Katoch V, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Scaria V, Sivasubbu S.                                                                               Genome Announc.(2013);1(6).

          17. Draft Genome Sequence of Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolate OSDD515, Belonging to the Uganda I Genotype. Vellarikkal SK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Sivasubbu S, Scaria V.                                                                                                 Genome Announc.(2013);1(6).

          18. Draft Genome Sequence of a Multidrug-Resistant Clinical Isolate of Mycobacterium tuberculosis Belonging to a Novel Spoligotype. Vellarikkal SK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Sivasubbu S, Scaria V.                                                                                                        Genome Announc. (2013); 1(6)

          19. 3D-QSAR studies and shape based virtual screening for identification of novel hits to inhibit MbtA in Mycobacterium tuberculosis. Maganti L; OSDD Consortium, Ghoshal N.           J Biomol Struct Dyn.(2015);33(2):344-64.

          20.Tumor homing peptides as molecular probes for cancer therapeutics, diagnostics and theranostics. Gautam A, Kapoor P, Chaudhary K, Kumar R; Open Source Drug Discovery Consortium, Raghava GP.                                                                                       Curr Med Chem. (2014);21(21):2367-91.

          21. g_mmpbsa—a GROMACS tool for high-throughput MM-PBSA calculations. Kumari R, Kumar R; Open Source Drug Discovery Consortium, Lynn A.                                              J Chem Inf Model. (2014);54(7):1951-62.

          22. QSAR-based models for designing quinazoline/imidazothiazoles/pyrazolopyrimidines based inhibitors against wild and mutant EGFR. Chauhan JS, Dhanda SK, Singla D; Open Source Drug Discovery Consortium, Agarwal SM,Raghava GP.                                      PLoS One.(2014);9(7)

          23. Data-mining of potential antitubercular activities from molecular ingredients of traditional Chinese medicines. Jamal S, Scaria V; Open Source Drug Discovery Consortium.   PeerJ. (2014);2:e476.

 24. BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extra. Sharma , Dutta P, Sharma M, Rajput NK, Dodiya B, Georrge JJ, Kholia T; OSDD Consortium, Bhardwaj A.                                                                                    J Cheminform.(2014); 6(1): 46.

          25. HGV&TB: a comprehensive online resource on human genes and genetic variants associated with tuberculosis. Sahajpal R, Kandoi G, Dhiman H, Raj S; Open Source Drug Discovery Consortium,Scaria V, Bhartiya D, Hasija Y.                                           Database (Oxford). (2014)

           26. Cheminformatics models for inhibitors of Schistosoma mansoni thioredoxin glutathione reductase. Gaba S, Jamal S, Open Source Drug Discovery Consortium, Scaria V.                   ScientificWorld Journal (2014).

           27.MetaNET--a web-accessible interactive platform for biological metabolic network analysis. Narang P, Khan S, Hemrom AJ; Open Source Drug Discovery Consortium, Lynn AM. BMC Syst Biol. (2014);8:130.

           28. Structure-based design of diverse inhibitors of Mycobacterium tuberculosis N-acetylglucosamine-1-phosphate uridyltransferase: combined molecular docking, dynamic simulation, and biological activity. Soni V, Suryadevara P, Sriram D; OSDD Consortium, Kumar S, Nandicoori VK, Yogeeswari P.                                                                         J Mol Model.(2015);21(7):174.

 29. Open Source Software and Web Services for Designing Therapeutic Molecules.

Singla D, Dhanda SK, Chauhan JS, Bhardwaj A, Brahmachari SK; Open Source Drug Discovery Consortium, Raghava GP. 
Curr Top Med Chem. 2013 May 1;13(10):1172-91

Publications by Dr. Brahmachari’s Students and Associates under his Mentorship
(Where Dr. Brahmachari is not an author)

1. A new polymer supported packing material as a substitute of Hydroxylapatite:Purification of Topoisomerases.
K.Majumder and N.Ramesh.
Chromatographia (1987) 24:400 

2. Preparation and characterisation of a new Matrix: Polymer supported Hydroxlapatite Substitute. Majumder, K. 
Biol.Chem. Hoppe-Seyler (1987) 368: 760 

3. Screening of clones containing altered DNA conformations by plasmid topoprofile shift. 
N.Ramesh and R.K.Mishra.
J. Biochem. Biophys. Meth. (1991) 22: 171 

4. Hereditary ataxia with ophthalmoplegia-preliminary observations on a Bengali family with autosomal dominant inheritance. 
Ambar Chakravarty, Angshuman Mukerjee, Somaditya Banerjee and Quasar Saleem.
J. of Association of Neuroscientists of Eastern India (1996) 1:188 

5. Molecular Analysis of Friedreich’s Ataxia locus in the Indian Population. 
M.Mukerji, S. Choudhry, Q.Saleem, M.V.Padma, M.C. Maheshwari, S. Jain 
Acta Neurologica Scandinavica (2000) 102-4 227:229 

6. Sample Size considerations in genetic polymorphism studies. 
Chandrika B. Rao.
Human Heredity (2001) 52(4): 191-200 

7. Spectrum of b-thalassaemia mutations and their association with allelic sequence polymorphisms at the b-globin gene cluster in eastern Indian population 
Ritushree Kukreti, Debasis Dash, Vineetha K E, Sanchita Chakravarty, Swapan Kr Das, Madhusnata De, Geeta Talukder.
American Journal of Hematology (2002) 70(4): 269-77 

8. Origin and instability of GAA repeats: insights from Alu elements.
Chauhan C, Dash D, Grover D, Rajamani J, Mukerji M.
J Biomol Struct Dyn. (2002) 20(2): 253-63 

9. SMARCA2 and THAP11: potential candidates for polyglutamine disorders as evidenced from polymorphism and protein-folding simulation studies 
Pandey N, Mittal U, Srivastava AK, Mukerji M 
J Hum Genet. (2004) 49(11): 596-602 

10. In silico characterization of the INO80 subfamily of SWI2/SNF2 chromatin remodeling proteins. 
Bakshi R, Prakash T, Dash D, Brahmachari V. 
Biochem Biophys Res Commun. (2004) 320(1): 197-2 

11. Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins.
Pandey N, Ganapathi M, Kumar K, Dasgupta D, Sutar SD, Dash D.
Bioinformatics. (2004) 20(17): 2904-10 

12. SMARCA2 and THAP11: potential candidates for polyglutamine disorders as evidenced from polymorphism and protein-folding simulation studies.
Pandey N, Mittal U, Srivastava AK, Mukerji M.
J Hum Genet. 2004; 49(11):596-602

13. ArrayD: a general purpose software for microarray design.
Sharma A, Srivastava GP, Sharma VK, Ramachandran S.
BMC Bioinformatics (2004) 2(5): 142

14. Founder Haplotype for Machado-Joseph Disease in the Indian Population: Novel Insights from History and Polymorphism Studies.
Uma Mittal; Achal K. Srivastava; Satish Jain; Sanjeev Jain; Mitali Mukerji.
Arch Neurol (2005) 62 :637-640

15. Post-zygotic de novo trinucleotide repeat expansion at spinocerebellar ataxia type 7 locus: evidence from an Indian family.
Mittal U, Roy S, Jain S, Srivastava AK, Mukerji M.
J Hum Genet. (2005) 50(3):155-7

16. Evidence of a Common Founder for SCA12 in the Indian Population.
S. Bahl K. Virdi, U. Mittal, M. P. Sachdeva, A. K. Kalla, S. E. Holmes, E. O'Hearn, R. L. Margolis, S. Jain, A. K. Srivastava and M. Mukerji.
Ann Hum Genet. (2005) 69(5): 528-34

17. Insights into the mutational history and prevalence of SCA1 in the Indian population through anchored polymorphisms.
Mittal U, Sharma S, Chopra R, Dheeraj K, Pal PK, Srivastava AK, Mukerji M.
Hum Genet. (2005) 118(1):107-14

18. SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks.
Sachdeva G, Kumar K, Jain P, Ramachandran S.
Bioinformatics (2005) 21(4): 483-91

19. Intrinsic unstructuredness and abundance of PEST motifs in eukaryotic proteomes.
Singh GP, Ganapathi M, Sandhu KS, Dash D.
Proteins (2006) 62(2):309-15

20. Simple sequence proteins in prokaryotic proteomes.
Subramanyam MB, Gnanamani M, Ramachandran S.
BMC Genomics (2006) 8(7): 141

21. Conformational flexibility may explain multiple cellular roles of PEST motifs.
Sandhu KS, Dash D.
Proteins (2006) 63(4): 727-32.

22. DyNAVacS: an integrative tool for optimized DNA vaccine design.
Harish N, Gupta R, Agarwal P, Scaria V, Pillai B.
Nucleic Acids Res. (2006) 34(Web Server issue):W264-6

23. Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences.
Scaria V, Hariharan M, Arora A, Maiti S.
Nucleic Acids Res. (2006) 34(Web Server issue):W683-5

24. Pharmacogenomics of beta2-agonist: key focus on signaling pathways. Bhatnagar P, Guleria R, Kukreti R.
Pharmacogenomics (2006) 7(6): 919-33

25. Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of diVerent functional categories.
Ravi Shankar, Amit Chaurasia, Biswaroop Ghosh, Dmitry Chekmenev, Evgeny Cheremushkin, Alexander Kel, Mitali Mukerji.
Mol Genet Genomics (2007) 277: 441–455

26. microRNAs in viral oncogenesis 
Scaria V, Jadhav V 
Retrovirology (2007) 4: 82 

27. Inhibition of translation in living eukaryotic cells by an RNA G-quadruplex motif 
Arora A, Dutkiewicz M, Scaria V, Hariharan M, Maiti S, Kurreck J 
RNA (2008) 14 (7): 1290-6 

28. MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic {beta}-actin gene. 
Ghosh T, Soni K, Scaria V, Halimani M, Bhattacharjee C, Pillai B 
Nucleic Acids Res. (2008) 36(19): 6318-32 

29. Antagomirzymes: oligonucleotide enzymes that specifically silence microRNA function 
Jadhav VM, Scaria V, Maiti S 
Angew Chem Int Ed Engl. (2009) 48(14): 2557-60 

30. Upregulation of miR-23a-27a-24-2 cluster induces caspase-dependent and -independent apoptosis in human embryonic kidney cells 
Chhabra R, Adlakha YK, Hariharan M, Scaria V, Saini N. 
PLoS One (2009) 4 (6): e5848 

31. Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features 
Kumar S, Ansari FA, Scaria V 
Virol J. (2009) 6: 129 

32. MicroRNAs: novel therapeutic targets in neurodegenerative diseases 
Roshan R, Ghosh T, Scaria V, Pillai B 
Drug Discov Today (2009) 14(23-24): 1123-9 

33. Consensus miRNA expression profiles derived from interplatform normalization of microarray data. 
Bargaje R, Hariharan M, Scaria V, Pillai B 
RNA (2010) 16(1): 16-25 

34. Absence of a general association between ABCB1 genetic variants and response to antiepileptic drugs in epilepsy patients 
Grover S, Bala K, Sharma S, Gourie-Devi M, Baghel R, Kaur H, Gupta M, Talwar P, Kukreti R. 
Biochimie. (2010) 92(9): 1207-12 

35. Modulation of microRNA function by synthetic ribozymes 
Suryawanshi H, Scaria V, Maiti S 
Mol Biosyst. (2010) 6(10): 1807-9 

36. Genetic polymorphisms in sex hormone metabolizing genes and drug response in women with epilepsy 
Grover S, Talwar P, Gourie-Devi M, Gupta M, Bala K, Sharma S, Baghel R, Kaur H, Sharma A, Kukreti R 
Pharmacogenomics (2010) 11(11): 1525-34 

37. Locked onto the target: increasing the efficiency of antagomirzymes using locked nucleic acid modifications 
Kaur H, Scaria V, Maiti S 
Biochemistry (2010) 49(44): 9449-56 

38. Genetic polymorphisms of drug-metabolizing phase I enzymes CYP2E1, CYP2A6 and CYP3A5 in South Indian population
Krishnakumar D, Gurusamy U, Dhandapani K, Surendiran A, Baghel R, Kukreti R, Gangadhar R, Prayaga U, Manjunath S, Adithan C 
Fundam Clin Pharmacol. (2011) 26(2): 295-306 

39. miRvar: A comprehensive database for genomic variations in microRNAs 
Bhartiya D, Laddha SV, Mukhopadhyay A, Scaria V 
Hum Mutat. (2011) 32(6): E2226-45 

40. Challenges and recommendations for conducting epidemiological studies in the field of epilepsy pharmacogenetics. 
Grover S, Gupta M, Kukreti R. 
Indian J Hum Genet. (2011)17 Suppl 1:S4-S11 

41. Genetic polymorphism of drug refractory epilepsy. 
Kesavan R, Kukreti R, Adithan C. 
Indian J Med Res. 2011 Sep;134:253-5. 

 Ayurgenomics: a new way of threading molecular variability for stratified medicine.
Sethi TP, Prasher B, Mukerji M.
ACS Chem Biol. 2011 Sep 16;6(9):875-80.

43. Inter and intra-ethnic differences in the distribution of the molecular variants of TPMT, UGT1A1 and MDR1 genes in the South Indian population. 
Umamaheswaran G, Krishna Kumar D, Kayathiri D, Rajan S, Shewade DG, Dkhar SA, Manjunath S, Ushakiran P, Reneega G, Ritushree K, Adithan C. 
Mol Biol Rep. 2012 May;39(5):6343-51. 

44. Genetic polymorphisms and retention rate of antiepileptic drugs. 
Grover S, Kukreti R. 
Pharmacogenomics. 2012 Apr;13(5):519-24 

45.Genetic association analysis of transporters identifies ABCC2 loci for seizure control in women with epilepsy on first-line antiepileptic drugs. 
Grover S, Gourie-Devi M, Bala K, Sharma S, Kukreti R. 
Pharmacogenet Genomics. 2012 Jun;22(6):447-65. 

46. Functional genetic polymorphisms from phase-II drug metabolizing enzymes. 
Grover S, Kukreti R. 
CNS Neurosci Ther. 2012 Aug;18(8):705-6. 

47. Curcumin prevents formation of polyglutamine aggregates by inhibiting Vps36, a component of the ESCRT-II complex. 
Verma M, Sharma A, Naidu S, Bhadra AK, Kukreti R, Taneja V. 
PLoS One. 2012;7(8):e42923. 

48. Genetic studies indicate a potential target 5-HTR(3B) for Drug Therapy in Schizophrenia Patients. 
Gupta M, Jain S, Moily NS, Kaur H, Jajodia A, Purushottam M, Kukreti R. 
Am J Med Genet B Neuropsychiatr Genet. (2012)159B(8):1006-8 

49. De novo identification of viral pathogens from cell culture hologenomes. 
Patowary A, Chauhan RK, Singh M, Kv S, Periwal V, Kp K, Sapkal GN, Bondre VP, Gore MM, Sivasubbu S, Scaria V. 
BMC Res Notes. (2012) 5:11. 

50. Potential G-quadruplexes in the human long non-coding transcriptome. 
Jayaraj GG, Pandey S, Scaria V, Maiti S. 
RNA Biol. (2012) 9(1):81-6 

51. Antagonism of microRNA function in zebrafish embryos by using locked nucleic acid enzymes (LNAzymes). 
Suryawanshi H, Lalwani MK, Ramasamy S, Rana R, Scaria V, Sivasubbu S, Maiti S. 
Chembiochem. (2012) 13(4):584-9. 

52. High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. 
Sati S, Tanwar VS, Kumar KA, Patowary A, Jain V, Ghosh S, Ahmad S, Singh M, Reddy SU, Chandak GR, Raghunath M, Sivasubbu S, Chakraborty K, Scaria V, Sengupta S. 
PLoS One. (2012) 7(2):e31621 

53. Systematic analysis and functional annotation of variations in the genome of an Indian individual. 
Patowary A, Purkanti R, Singh M, Chauhan RK, Bhartiya D, Dwivedi OP, Chauhan G, Bharadwaj D, Sivasubbu S, Scaria V. 
Hum Mutat. (2012)33(7):1133-40. 

54. A case for pharmacogenomics in management of cardiac arrhythmias. 
Kandoi G, Nanda A, Scaria V, Sivasubbu S. 
Indian Pacing Electrophysiol J. (2012) 12(2):54-64 

55. Conceptual approaches for lncRNA drug discovery and future strategies. 
Bhartiya D, Kapoor S, Jalali S, Sati S, Kaushik K, Sachidanandan C, Sivasubbu S, Scaria V. 
Expert Opin Drug Discov. (2012) 7(6):503-13 

56. Presence of strong association of the major histocompatibility complex (MHC) class I allele HLA-A*26:01 with idiopathic hypoparathyroidism. 
Goswami R, Singh A, Gupta N; Indian Genome Variation Consortium, Rani R. 
J Clin Endocrinol Metab. (2012) 97(9):E1820-4 

57. Systematic curation and analysis of genomic variations and their potential functional consequences in snoRNA loci. 
Bhartiya D, Talwar J, Hasija Y, Scaria V. 
Hum Mutat. (2012) 33(10):E2367-7 

58. Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain. 
Bargaje R, Alam MP, Patowary A, Sarkar M, Ali T, Gupta S, Garg M, Singh M, Purkanti R, Scaria V, Sivasubbu S, Brahmachari V, Pillai B. 
Nucleic Acids Res. (2012) 40(18):8965-78 

59. Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. 
Jalali S, Jayaraj GG, Scaria V. 
Biol Direct. (2012) 7:25. 

60. Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. 
Sati S, Ghosh S, Jain V, Scaria V, Sengupta S. 
Nucleic Acids Res. (2012) 40(20):10018-31 

61. MitoLSDB: A Comprehensive Resource to Study Genotype to Phenotype Correlations in Human Mitochondrial DNA Variation.
S. Mole, S. Jalali, V. Scaria, A. Bhardwaj 
PLoS ONE 2013 (in press)