2025
71. Mohapatra A, Kadumuri RV, Sharma A, Saju AP, Ramadasan H, Agrawal A, Sharma V, Chavali S*. Molecular attributes of intrinsically disordered regions in secretomes influence fungal pathogenesis. bioRxiv. 2025; https://doi.org/10.1101/2025.10.01.679754
70. Nair AU, Vishwakarma S, Guha T, Kadumuri RV, Fritschi F, Chavali S*, Allu AD*. ERF transcription factor regulons underpin growth-defence trade-off under acute heat stress in rice seedlings. bioRxiv. 2025; https://doi.org/10.1101/2025.04.21.649784
69. Singh AK, Rachote N, Agrawal A, Sharma V, Kappaguntala KS, Kadumuri RV, Chavali S*. Amino acid repeats signature underlying human-pathogen interactions. bioRxiv. 2025; https://doi.org/10.1101/2025.03.17.643713
68. Krishnamoorthy VK, Arsala RR, Hamdani F, Shukla P, Anaitullah S, Biligiri KK, Kadumuri RV, Pothula PR, Chavali S, Rampalli S. NSD3 protein methylation and stabilization transforms human ES cells into variant state. Life Science Alliance. 2025: 8:e202402871.
DOI: 10.26508/lsa.202402871
2024
67. Ganguli S, Gupta D, Ramaswamy R, Kadumuri RV, Krishnan A, Tandel D, David DT, Bunk S, Chavali S, Krishnan HH, Chavali PL. RNA binding protein Musashi1 interacts with the viral genomic RNA and restricts SARS-CoV-2 infection by repressing translation. bioRxiv. 2024; https://doi.org/10.1101/2024.09.29.615653
66. Gupta S, Verma M, Kadumuri RV, Chutani N, Khan MIK, Chavali S*, Dhayalan A*. The uncharacterized protein ZNF200 interacts with PRMT3 and aids its stabilization and nuclear translocation. Biochemical Journal. 2024: 481: 1723–1740.
DOI: https://doi.org/10.1042/BCJ20240476
2023
65. Das KK, Mohapatra A, George AP, Chavali S, Witzel K, Ramireddy E. The proteome landscape of the root cap reveals a role for the jacalin-associated lectin JAL10 in the salt-induced endoplasmic reticulum stress pathway. Plant Communications. 2023; 4: 100726.
DOI: 10.1016/j.xplc.2023.100726
64. Eragam A, Mohapatra A, Shukla V, Kadumuri RV, George Ab, Putta L, Akkareddy S, Chavali S, Vemireddy LR, Ramireddy E. Panicle transcriptome of a high-yield mutant indica rice reveals physiological mechanisms and novel regulatory genes for yield under reproductive stage drought stress. BMC Plant Biology. 2023; 23: 493.
DOI: 10.1186/s12870-023-04507-1
63. Singh AK, Amar I, Ramadasan H, Kappaguntala KS, Chavali S*. Proteins with amino acid repeats constitute the rapidly evolvable and human-specific essentialome. Cell Reports. 2023; 42: 112811.
PUBMED: 37453061
62. Samantaray D, Vankanavath AB, Ramadurai D, Kadumuri RV, Chavali S, Allu AD. Thermopriming mitigates the effects of heat stress by modulating the expression of Heat Shock Factors in Brassica juncea (Indian mustard). Environmental and Experimental Botany. 2023; 211: 105371.
DOI: https://doi.org/10.1016/j.envexpbot.2023.105371
61. Rachote N, Agrawal A, Chavali PL, Chavali S*. RNA as Modulators of Infection Outcome: Potential Usage for Genomic Surveillance in Genomic Surveillance and Pandemic Preparedness, 2023 (Ed: Rajesh Pandey), Elsevier Academic Press.
60. Chavali PL, Singh AK, Chavali S*. Nuclear architecture and transcriptional regulation of microRNAs in MicroRNA in Regenerative Medicine, Second Edition, 2023 (Ed: Chandan Sen), Elsevier Academic Press.
2022
59. Chutani N, Singh AK, Kadumuri RV, Pakala SB, Chavali S*. Structural attributes and functional roles of Microrchidia family of chromatin remodelers. Journal of Molecular Biology. 2022; 434: 167664.
PUBMED: 35659506
58. Nair A, Bhukya DPN, Sunkar R, Chavali S, Allu AD. Molecular basis of priming-induced acquired tolerance to multiple abiotic stresses in plants. Journal of Experimental Botany. 2022; 73: 3355-71.
DOI: https://doi.org/10.1093/jxb/erac089
2021
57. Govindaraju G, Chavali S, Rajavelu A. Plasmodium falciparum YTH2 domain binds to m6A-containing mRNA and regulates translation. mBio 2021; 12: e0136721.
PUBMED: 34809465
56. Gupta S, Kadumuri RV, Singh AK, Chavali S, Dhayalan A. Structure, activity and function of the protein arginine methyltransferase 6. Life 2021; 11: 951.
PUBMED: 34575100
55. Khan MIKK, Charles RCM, Ramachandran R, Gupta S, Govindaraju G, Mishra R, Rajavelu A, Coumar MS, Chavali S*, Dhayalan A*. The ribosomal protein eL21 interacts with the protein lysine methyl transferase SMYD2 and regulates its steady state levels. Biochimica et Biophysica Acta - Molecular Cell Research. 2021; 1868: 119079.
PUBMED: 34147559
54. Chakrapani B, Khan MIK, Kadumuri RV, Verma M, Awasthi S, Govindaraju G, Mahesh A, Rajavelu A, Chavali S*, Dhayalan A*. The Uncharacterized protein, FAM47E interacts with PRMT5 and regulates its functions. Life Science Alliance 2021; e202000699.
PUBMED: 33376131
53. Verma M, Chakrapani B, Kadumuri RV, Awasthi S, Mahesh A, Govindaraju G, Chavali PL, Rajavelu A, Chavali S*, Dhayalan A*. PRMT3 interacts with ALDH1A1 and regulates gene expression regulation by inhibiting retinoic acid signaling. Communications Biology 2021;4:109.
PUBMED: 33495566
2020
52. Masuho I, Santhanam B, Skamangas NK, Chavali S, Tesmer JJG, Babu MM, Martemyanov KE. A complete map of G protein signaling regulation by RGS proteins. Cell 2020; 183:503-521.
PUBMED: 33007266
51. Govindaraju G, Kadumuri RV, Jabeena CA, Sethumadhavan DV, Chavali S, Rajavelu A. N 6 -Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum. Epigenetics & Chromatin 2020; 13:33.
DOI: https://doi.org/10.1186/s13072-020-00355-7
50. Sreenivas Chavali*, Anjali K. Singh, Balaji Santhanam & M. Madan Babu. Amino acid homorepeats in proteins. Nature Reviews Chemistry, 2020; 4, 420–434.
DOI: https://doi.org/10.1038/s41570-020-0204-1
49. Ravarani C, Flock T †† , Chavali S †† , Babu MM, Balaji S. Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation. Nature Communications 2020; 11: 2384.
PUBMED: 32404905
48. Mahesh A, Khan MIK, Govindaraju G, Verma M, Awasthi S, Chavali PL, Chavali S., Rajavelu A, Dhayalan. SET7/9 interacts and methylates the ribosomal proteins eL42 and regulates protein synthesis. Biochimica et Biophysica Acta - Molecular Cell Research 2020; 1867: 118611.
PUBMED: 31751593
47. Chavali PL, Ramachandran R, ,Chavali S*. Functional Categories of RNA regulation in RNA based regulation in Health and Disease, 2020 (Ed: Rajesh Pandey) Elsevier Academic Press.
DOI: https://doi.org/10.1016/B978-0-12-817193-6.00003-0
Prior to joining IISER Tirupati
2018
46. Awasthi S, Chakrapani B, Mahesh A, Chavali S , Dhayalan A. DDX39B promotes translation through regulation of pre-ribosomal RNA levels. RNA Biology 2018;15: 1157-1166.
PUBMED: 30176153
45. Mausho I, Chavali S,Skamangas NK, Simonyan K, Patil DN, Kramer GN, Ozelius L, Babu MM, Martemyanov KA. Molecular deconvolution platform to establish disease mechanisms by surveying GPCR signaling. Cell Reports 2018; 24: 557-68.
PUBMED: 30021154
44. Awasthi S, Verma M, Mahesh A, Khan MIK, Govindaraju G, Rajavelu A, Chavali PL, Chavali S*,Dhayalan A*. DDX49 is an RNA helicase that affects translation by regulating mRNA export and the levels of pre-ribosomal RNA. Nucleic Acids Research 2018; 46: 6304-17.
PUBMED: 29618122
43. Li X, Chavali PL, Pancsa R, Chavali S,Babu MM. Function and regulation of phase separated biological condensates. Biochemistry 2018; 57: 2452-61.
PUBMED: 29392932
42. Hauser A, Chavali S,Masuho I, Jahn LJ, Martemyanov KA, Gloriam DE, Babu MM. Pharmacogenomics of GPCR drug targets. Cell 2018; 172: 41-54.
PUBMED: 29249361
2017
41. Chavali S*,Chavali PL, Chalacon G, Sanchez de Groot N, Gemayel R, Latysheva NS, Ing- Simmons E, Verstrepen KJ, Balaji S, Babu MM. Constraints and consequences of the emergence of amino acid repeats in eukaryotic proteins. Nature Structural and Molecular Biology 2017; 24: 765-77.
PUBMED: 28805808
40. Verma M, Charles RCM, Chakrapani B, Coumar MS, Govindaraju G, Rajavelu A, Chavali S,Dhayalan A. PRMT7 interacts with ASS1 and citrullinemia mutations disrupt the interaction. Journal of Molecular Biology 2017; 429: 2278-89.
PUBMED: 28587924
39. Chavali S*,Gunnarsson A, Babu MM. Intrinsically disordered proteins adaptively reorganize cellular matter during stress. Trends in Biochemical Sciences 2017; 42: 410-12.
PUBMED: 28487210
2016
38. Yu H, Gautam AKS, Wilmington S, Wylie D, Martinez-Fonts K, Kago G, Warburton M, Chavali S,Inobe T, Finkelstein I, Babu MM, Matouschek A. Conserved sequence preferences contribute to substrate recognition by the proteasome. Journal of Biological Chemistry 2016; 291: 14526-39.
PUBMED: 27226608
37. Chavali PL, Chandrasekaran G, Barr AR, Tatrai P, Taylor C, Papachristou E, Woods GC, Chavali S,Gergely F. A CEP215-HSET complex links centrosomes with spindle poles and drives centrosome clustering in cancer. Nature Communications 2016; 17: 11005.
2015
36. Gemayel R, Chavali S,Zhu B, Legendre M, Boeynaems S, van der Zande E, Babu MM, Verstrepen KJ. Variable glutamine-rich repeats modulate function of the transcriptional regulator SSN6. Molecular Cell 2015; 59: 615-27. Research highlighted in Nature Reviews Molecular Cell Biology.
PUBMED: 26257283
35. Latysheva N, Flock T, Weatheritt RJ, Chavali S,Babu MM. How do disordered regions achieve functions comparable to structured domains?. Protein Science 2015; 24: 909-22.
PUBMED: 25752799
34. Fishbain S, Inobe T, Israeli E, Chavali S,Yu H, Kago G, Babu MM, Matouschek A. Sequence composition of disordered regions fine-tunes protein half-life. Nature Structural and Molecular Biology 2015; 22: 214-21.
PUBMED: 25643324
2014
33. Chavali PL, Chavali S*. Nuclear architecture and transcriptional regulation of microRNAs inMicroRNA in Regenerative. Medicine, 2014; (Ed: Chandan Sen), Elsevier Academic Press.
DOI: https://doi.org/10.1016/B978-0-12-405544-5.00043-5
2013
32. Chavali S*,Bruhn S, Tiemann K, Saetrom P, Barrenas F, Saito T, Kanduri K, Wang H, Benson M. microRNAs act complementarily to regulate disease-related mRNA modules in human diseases. RNA 2013; 19: 1552-62.
PUBMED: 24062574
31. Wickramasinghe VO † , Savill JM † , Chavali S,Jonsdottir AB, Rajendra E, Gruner T, Jeyasekharan AD, Laskey RA, Babu MM, Venkitaraman AR. Human inositol polyphosphate multikinase regulates transcript-selective nuclear mRNA export to preserve genome integrity. Molecular Cell 2013; 51: 737-50.
PUBMED: 24074953
30. Tabassum R, Chauhan G, Dwivedi OP, Mahajan A, Jaiswal A, Kaur I, Bandesh K, Chidambaram M, Sharma A, Chavali S, Bharadwaj D. Genome wide association study for type 2 diabetes in Indians identifies a new susceptibility locus at 2q21. Diabetes 2013; 62: 977-86.
PUBMED: 23209189
29. Chavali S*,Kanduri K. Network Medicine: Disease genes in molecular networks Statistical Diagnostics of Cancer: Analyzing High- dimensional Data, 2013 (Ed: Frank Emmert-Streib & Matthias Dehmer) Wiley-Blackwell.
DOI: https://doi.org/10.1002/9783527665471.ch8
2012
28. Barrenas F †, Chavali S †,Alves AC, Coin L, Jarvelin MR, Jörnsten R, Langston MA, Ramasamy A, Rogers G, Wang H, Benson M. Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms. Genome Biology 2012; 13: R46.
PUBMED: 22703998
27. Bruhn S, Barrenas F, Mobini R, Andersson BA, Chavali S ,Egan BS, Hovig E, Sandve GK, Langston MA, Rogers G, Wang H, Benson M. Increased expression of IRF4 and ETS1 in CD4(+) cells from patients with intermittent allergic rhinitis. Allergy 2012; 67: 33-40.
PUBMED: 21919915
2011
26. Chavali S, Mahajan A, Tabassum R, Dwivedi OP, Chauhan G, Ghosh S, Tandon N, Bharadwaj D. Association of variants in genes involved in pancreatic b-cell development and function with type 2 diabetes in North Indians. Journal of Human Genetics 2011; 56: 695-700.
PUBMED: 21814221
25. Chavali S*, Mahajan A, Ghosh S, Mondal B, Bharadwaj D. Protein molecular function influences mutation rates in human genetic diseases with allelic heterogeneity. Biochemical and Biophysical Research Communications 2011; 412: 716-22.
PUBMED: 21867677
24. Chavali PL, Funa K, Chavali S* . Cis-regulation of microRNA expression by Scaffold/Matrix attachment regions. Nucleic Acids Research 2011; 39: 6908-18.
PUBMED: 21586588
23. Chavali S*, de Lima Morias DA, Gough J, Babu MM. Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving evolving metazoan, Oikopleura dioica. Bioessays 2011; 33: 592-601.
PUBMED: 21681984
22. Wang H, Chavali S, Mobini R, Muraro A, Barbon F, Boldrin D, Aberg N, Benson M. A pathway-based approach to find novel markers of local glucocorticoid treatment in intermittent allergic rhinitis. Allergy 2011; 66: 132-140.
PUBMED: 20659080
21. Indian Diabetes Consortium ‡INDICO:the development of a resource for epigenomic study of Indians undergoing socioeconomic transition. The HUGO Journal 2011; 5: 65-9.
PUBMED: 23205164
20. Mahajan A, Tabassum R, Chavali S ,Dwivedi OP, Chauhan G, Ghosh S, Tandon N, Bharadwaj D. Common variants in CRP and LEPR influence high sensitivity C-reactive protein levels in North Indians. PLoS ONE 2011; 6: e24645.
PUBMED: 21931794
2010
19. Chauhan G, Spurgeon CJ, Tabassum R, Bhaskar S, Kulkarni SJ, Mahajan A, Chavali S, Bharadwaj D. Impact of common variants of PPARG, KCNJ11, TCF7L2, SLC30A8, HHEX, CDKN2A, IGF2BP2 and CDKAL1 on the risk of type 2 diabetes in 5148 Indians. Diabetes 2010; 59: 2068-74.
PUBMED: 20424228
18. Mahajan A, Tabassum R, Chavali S, Dwivedi OP, Chauhan G, Tandon N, Bharadwaj D. Obesity-dependent association of TNF-LTA locus with type 2 diabetes in North Indians. Journal of Molecular Medicine 2010; 88: 515-22.
PUBMED: 20177654
17. Sharma A † , Chavali S † , Tabassum R, Tandon N, Bharadwaj D. Gene prioritization in Type 2 Diabetes using domain interactions and network analysis. BMC Genomics 2010; 11: 84.
PUBMED: 20122255
16. Pavithra L, Chavali S, Chattopadhyay S. Nutritional epigenetics: impact on metabolic syndrome in Nutrition, Epigenetic Mechanisms, and Human Disease, 2010 (Ed: Nilanjana Maulik & Gautam Maulik) CRC press, USA.
2009
15. Barrenas F † , Chavali S † , Holme P, Mobini R, Benson M. Network properties of complex human disease genes identified through genome-wide association studies. PLoS ONE 2009; 4: e8090.
PUBMED: 19956617
14. Chavali S ,Ghosh S, Bharadwaj D. Hemophilia B as a quasi-quantitative condition with certain mutations showing phenotypic plasticity. Genomics 2009; 94 : 433-7.
PUBMED: 19699296
13. Mahajan A, Tabassum R, Chavali S ,Dwivedi OP, Bharadwaj M, Tandon N, Bharadwaj D. High sensitivity C-reactive protein and Type 2 Diabetes in urban North Indians. Journal of Clinical Endocrinology and Metabolism 2009; 94: 2123-7.
PUBMED: 19336513
2008
12. Tabassum R, Chavali S, Mahajan A, Ghosh S, Tandon N, Madhu SV, Bharadwaj D. Association analysis of TNFRSF1B polymorphisms with Type 2 Diabetes and its related traits in North India. Genomic Medicine 2008; 2: 93-100.
PUBMED: 19343543
11. Tabassum R, Chavali S ,Dwivedi OP, Tandon N, Bharadwaj D. Genetic variants of FOXA2: risk of type 2 diabetes and effect on metabolic traits in North Indians. Journal of Human Genetics 2008; 53: 957-65.
PUBMED: 18797817
10. The Indian Genome Variation Consortium ‡Genetic Landscape of the People of India: a Canvas for Disease Gene Exploration. Journal of Genetics 2008; 87: 3-20.
PUBMED: 18560169
9. Chavali S*,Sharma A, Tabassum R, Bharadwaj D. Sequence and structural properties of identical mutations leading to varying phenotypes in human coagulation factor IX. Proteins: Structure, Function and Bioinformatics 2008; 73: 63-71. Research highlighted in International Monitor on Hemophilia (Lillicrap D, Vol. 7, 2009)
PUBMED: 18393396
8. Sharma A † , Chavali S†,Mahajan A, Biswas P, Bharadwaj D. Multiple substitutions at single site- interpreting the effect of Asn92 mutations in human coagulation factor IX. Haemophilia 2008; 14: 396-9.
PUBMED: 18179572
2007
7. Mahajan A †, Chavali S†,Ghosh S, Kabra M, Chowdhury MR; Indian Genome Variation Consortium, Bharadwaj D. Allelic heterogeneity of molecular events in human coagulation factor IX in Asian Indians. Human Mutation 2007; 28: 526.
PUBMED: 17397055
2005
6. The Indian Genome Variation Consortium ‡The Indian Genome Variation database (IGVdb): a project review. Human Genetics 2005; 118: 1-11.
PUBMED: 16133172
5. Chavali S, Mahajan A, Tabassum R, Maiti S, Bharadwaj D. Oligonucleotide properties determination and Primer designing: A critical examination of predictions. Bioinformatics 2005; 21: 3918-25.
PUBMED: 16105896
4. Bharadwaj D, Chavali S,Mahajan A, Tabassum R, Sharma A. Genetic Studies in Type 2 Diabetes Mellitus: A time to rethink our strategies! (eLetter to the Editor). Molecular & Cellular Proteomics 2005.
3. Sharma A†, Chavali S† ,Mahajan A, Tabassum R, Banerjee V, Tandon N, Bharadwaj D. Genetic association, post-translational modification and protein-protein interactions in type 2 diabetes mellitus. Molecular & Cellular Proteomics 2005; 4: 1029-37.
2004
2. Mahajan A, Sharma A, Chavali S,Kabra M, Chowdhury MR, Srinivasan N, Bharadwaj D. Novel missense mutation in the coagulation factor IX catalytic domain associated with severe haemophilia B-Factor IXDelhi. Haemophilia 2004; 10: 550-2.
1. Mahajan A, Chavali S,Kabra M, Chowdhury MR, Bharadwaj D. Molecular characterization of hemophilia B in North Indian families: identification of novel and recurrent molecular events in the factor IX gene. Haematologica 2004; 89: 1498-503.