Google scholar: https://scholar.google.com/citations?user=WsKZ8IwAAAAJ&hl=en
*Corresponding Author; †Equal Contribution; ‡Consortium Member and Contributing author
2026
74. Singh AK, Babu A, Gopalakrishnan AS, Rachote N, Sharma V, Ganguli S, Kappagantula KS, Ramadasan H, Shukla P, Dhayalan A, Chavali PL, Chavali S*. Amino acid repeat mosaics shape protein functional landscape. bioRxiv. 2026
https://www.biorxiv.org/content/10.64898/2026.06.09.730932v1
73. Prashanth AK, Bhardwaj A, Kadumuri RV, Chavali S, Chalamcharla VR. Transcription termination safeguards quiescent chromatin for faithful cell-cycle re-entry. bioRxiv. 2026
https://www.biorxiv.org/content/10.64898/2026.03.28.714970v1
72. Nair AU, Vishwakarma S, Guha T, Kadumuri RV, Fritschi FB, Chavali S*, Allu AD*. Ethylene-jasmonate interplay involving ERF regulons modulates acute heat stress response in rice seedlings. The Plant Journal. 2026; 126: e70850.
https://onlinelibrary.wiley.com/doi/10.1111/tpj.70850
71. Ganguli S, Gupta D, Kadumuri RV, Tandel D, Ramaswamy R, Krishnan AG, David DT, Bunk S, Chavali S, Harshan KH, Chavali PL. RNA binding protein Musashi1 interacts with the viral genomic RNA and restricts SARS-CoV-2 infection by repressing translation. Nucleic Acids Research. 2026; 54: gkag271.
https://academic.oup.com/nar/article/54/6/gkag271/8566096
70. Singh AK, Rachote N, Sharma V, Agrawal A, Kappaguntala KS, Kadumuri RV, Chavali S*. Amino acid repeat signatures underlying human-pathogen interactions. iScience. 2026; 29: 115249
https://www.cell.com/iscience/fulltext/S2589-0042(26)00624-3
69. Bheemireddy S, Menon R, Chavali S, Sowdhamini R, Srinivasan N. Computational analyses of bifurcated inter-protein interactions in protein-protein assemblies reveal their pivotal role in conferring stability. Proteins: Structure, Function and Bioinformatics. 2026; 94: 987-998.
https://onlinelibrary.wiley.com/doi/10.1002/prot.70090
2025
68. Mohapatra A, Kadumuri RV, Sharma A, Saju AP, Ramadasan H, Agrawal A, Chavali S*. Molecular attributes of intrinsically disordered regions in secretomes influence fungal pathogenesis. bioRxiv. 2025
https://www.biorxiv.org/content/10.1101/2025.10.01.679754v1
2024
67. 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. 2024; 8: e202402871.
https://www.life-science-alliance.org/content/8/3/e202402871
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.
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.
https://www.cell.com/plant-communications/fulltext/S2590-3462(23)00272-9
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.
https://link.springer.com/article/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.
https://www.cell.com/cell-reports/fulltext/S2211-1247(23)00822-7
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.
https://www.sciencedirect.com/science/article/abs/pii/S0098847223001661
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.
https://www.sciencedirect.com/science/chapter/edited-volume/abs/pii/B9780443187698000040
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.
https://www.sciencedirect.com/science/chapter/edited-volume/abs/pii/B9780128207192000363
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.
https://www.sciencedirect.com/science/article/abs/pii/S002228362200256X
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.
https://academic.oup.com/jxb/article/73/11/3355/6546984
2021
57. Govindaraju G, Chavali S, Rajavelu A. Plasmodium falciparum YTH2 domain binds to m6A-containing mRNA and regulates translation. mBio 2021; 12: e0136721.
https://journals.asm.org/doi/10.1128/mbio.01367-21
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.
https://www.mdpi.com/2075-1729/11/9/951
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.
https://www.sciencedirect.com/science/article/pii/S0167488921001336
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; 4: e202000699.
https://www.life-science-alliance.org/content/4/3/e202000699
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.
https://www.nature.com/articles/s42003-020-01644-3
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.
https://www.cell.com/cell/fulltext/S0092-8674(20)31140-5
51. Govindaraju G, Kadumuri RV, Jabeena CA, Sethumadhavan DV, Chavali S, Rajavelu A. N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum. Epigenetics & Chromatin 2020; 13: 33.
https://link.springer.com/article/10.1186/s13072-020-00355-7
50. Chavali S*, Singh AK, Balaji S, Babu MM. Amino acid homorepeats in proteins. Nature Reviews Chemistry 2020; 4: 420-434. (With Cover image).
https://www.nature.com/articles/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.
https://www.nature.com/articles/s41467-020-16182-z
48. Mahesh A, Khan MIK, Govindaraju G, Verma M, Awasthi S, Chavali PL, Chavali S, Rajavelu A, Dhayalan A. SET7/9 interacts and methylates the ribosomal proteins eL42 and regulates protein synthesis. Biochimica et Biophysica Acta - Molecular Cell Research 2020; 1867: 118611.
https://www.sciencedirect.com/science/article/pii/S0167488919302198
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.
https://www.sciencedirect.com/science/chapter/edited-volume/abs/pii/B9780128171936000030
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.
https://www.tandfonline.com/doi/full/10.1080/15476286.2018.1517011
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.
https://www.cell.com/cell-reports/fulltext/S2211-1247(18)31007-6
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.
https://academic.oup.com/nar/article/46/12/6304/4956647
43. Li X, Chavali PL, Pancsa R, Chavali S, Babu MM. Function and regulation of phase separated biological condensates. Biochemistry 2018; 57: 2452-61.
https://pubs.acs.org/doi/10.1021/acs.biochem.7b01228
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.
https://www.cell.com/cell/references/S0092-8674(17)31384-3
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.
https://www.nature.com/articles/nsmb.3441
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.
https://www.sciencedirect.com/science/article/pii/S0022283617302693
39. Chavali S*, Gunnarsson A, Babu MM. Intrinsically disordered proteins adaptively reorganize cellular matter during stress. Trends in Biochemical Sciences 2017; 42: 410-12.
https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(17)30087-7
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.
https://www.sciencedirect.com/science/article/pii/S0021925820349127
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.
https://www.nature.com/articles/ncomms11005
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.
https://www.cell.com/molecular-cell/fulltext/S1097-2765(15)00534-1
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.
https://onlinelibrary.wiley.com/doi/10.1002/pro.2674
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.
https://www.nature.com/articles/nsmb.2958
2014
33. Chavali PL, Chavali S*. Nuclear architecture and transcriptional regulation of microRNAs in MicroRNA in Regenerative Medicine, 2014; (Ed: Chandan Sen), Elsevier Academic Press.
https://shop.elsevier.com/books/microrna-in-regenerative-medicine/sen/978-0-12-405544-5
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 modules in human diseases. RNA 2013; 19: 1552-62.
https://rnajournal.cshlp.org/content/19/11/1552.long
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.
https://www.cell.com/molecular-cell/fulltext/S1097-2765(13)00631-X
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.
29. Chavali S*, Kanduri K. Network Medicine: Disease genes in molecular networks in Statistical Diagnostics of Cancer: Analyzing High- dimensional Data, 2013 (Ed: Frank Emmert-Streib & Matthias Dehmer), Wiley-Blackwell.
https://onlinelibrary.wiley.com/doi/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.
https://link.springer.com/article/10.1186/gb-2012-13-6-r46
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. doi: 10.1111/j.1398-9995.2011.02707.x.
https://onlinelibrary.wiley.com/doi/10.1111/j.1398-9995.2011.02707.x
2011
26. Indian Diabetes Consortium‡. INDICO: the development of a resource for epigenomic study of Indians undergoing socioeconomic transition. The HUGO Journal 2011; 5: 65-9.
https://link.springer.com/article/10.1007/s11568-011-9157-2
25. 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.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024645
24. 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.
https://www.sciencedirect.com/science/article/abs/pii/S0006291X11014239
23. 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.
https://www.nature.com/articles/jhg201183
22. 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.
https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201100034
21. Chavali PL, Funa K, Chavali S*. Cis-regulation of microRNA expression by Scaffold/Matrix attachment regions. Nucleic Acids Research 2011; 39: 6908-18.
https://academic.oup.com/nar/article/39/16/6908/2411405
20. 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.
https://onlinelibrary.wiley.com/doi/full/10.1111/j.1398-9995.2010.02444.x
2010
19. Chavali S*, Barrenas F, Kanduri K, Benson M. Network properties of human disease genes with pleiotropic effects. BMC Systems Biology 2010; 4: 78.
https://link.springer.com/article/10.1186/1752-0509-4-78
18. 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.
https://doi.org/10.2337/db09-1386
17. 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.
https://link.springer.com/article/10.1007/s00109-010-0594-5
16. 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.
https://link.springer.com/article/10.1186/1471-2164-11-84
15. 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.
https://doi.org/10.1201/b10449
2009
14. 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.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008090
13. Chavali S, Ghosh S, Bharadwaj D. Hemophilia B as a quasi-quantitative condition with certain mutations showing phenotypic plasticity. Genomics 2009; 94 : 433-7.
https://www.sciencedirect.com/science/article/pii/S0888754309001852
12. 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.
https://academic.oup.com/jcem/article-abstract/94/6/2123/2597228
2008
11. 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.
https://pmc.ncbi.nlm.nih.gov/articles/PMC2694862/
10. 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.
https://www.nature.com/articles/jhg2008123
9. The Indian Genome Variation Consortium‡. Genetic Landscape of the People of India: a Canvas for Disease Gene Exploration. Journal of Genetics 2008; 87: 3-20.7.
https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.22035
8. 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.
https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.22035
7. 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.
https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2516.2007.01637.x
2007
6. 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.
https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.9494
2005
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.
https://academic.oup.com/bioinformatics/article/21/20/3918/203082
4. The Indian Genome Variation Consortium‡. The Indian Genome Variation database (IGVdb): a project review. Human Genetics 2005; 118: 1-11.
https://link.springer.com/article/10.1007/s00439-005-0009-9
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. https://www.sciencedirect.com/science/article/pii/S1535947620309762
2004
2. 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.
https://haematologica.org/article/view/3311
-
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. https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2516.2004.00948.x