Publications
2023
39. Nidhi Malhotra, Shantanu Khatri, Ajit Kumar, Akanksha Arun, Purba Daripa, Saman Fatihi, Sureshkumar Venkadesan, Niyati Jain & Lipi Thukral (2023)AI-based AlphaFold2 significantly expands the structural space of the autophagy pathway , Autophagy, 19:12, 3201-3220, DOI: 10.1080/15548627.2023.2238578 2023
2022
38. Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda Lorenzo Subissi, Anne von Gottberg, Lipi Thukral, Nathalie Worp, Bas B. Oude Munnink, Surabhi Rathore, Laith J. Abu-Raddad, Ximena Aguilera, Erik Alm, Brett N. Archer, Homa Attar Cohen, Amal Barakat, Wendy S. Barclay, Jinal N. Bhiman, Leon Caly, Meera Chand, Mark Chen, Ann Cullinane, Tulio de Oliveira, Christian Drosten, Julian Druce, Paul Effler, Ihab El Masry, Adama Faye, Simani Gaseitsiwe, Elodie Ghedin, Rebecca Grant, Bart L. Haagmans, Belinda L. Herring, Shilpa S. Iyer, Zyleen Kassamali, Manish Kakkar, Rebecca J. Kondor, Juliana A. Leite, Yee-Sin Leo, Gabriel M. Leung, Marco Marklewitz, Sikhulile Moyo, Jairo Mendez-Rico, Nada M. Melhem, Vincent Munster, Karen Nahapetyan, Djin-Ye Oh, Boris I. Pavlin, Thomas P. Peacock, Malik Peiris, Zhibin Peng, Leo L. M. Poon, Andrew Rambaut, Jilian Sacks, Yinzhong Shen, Marilda M. Siqueira, Sofonias K. Tessema, Erik M. Volz, Volker Thiel, Sylvie van der Werf, Sylvie Briand, Mark D. Perkins, Maria D. Van Kerkhove, Marion P. G. Koopmans & Anurag Agrawal. An early warning system for emerging SARS-CoV-2 variants. Nature Medicine. 2022 6.
37. Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer KB, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, Marco Ad, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity. Nature. 2022 603:706-714.
36. Pathak AK, Mishra GP, Uppili B, Walia S, Fatihi S, Abbas T, Banu S, Ghosh A, Kanampalliwar A, Jha A, Fatma S, Aggarwal S, Dhar MS, Marwal R, Radhakrishnan VS, Ponnusamy K, Kabra S, Rakshit P, Bhoyar RC, Jain A, Divakar MK, Imran M, Faruq M, Sowpati DT, Thukral L, Raghav SK, Mukerji M. Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. Nucleic Acids Research. 2022 50:1551-1561.
2021
35. Dhar MS, Marwal R, Radhakrishnan VS, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V, Naushin S, Rophina M, Mellan TA, Mishra S, Whittaker C, Fatihi S, Datta M, Singh P, Sharma U, Ujjainiya R, Bhatheja N, Divakar MK, Singh MK, Imran M, Senthivel V, Maurya R, Jha N, Mehta P, Sharma P, Arvinden VR, Chaudhary U, Soni N, Thukral L, Flaxman S, Bhatt S, Pandey R, Dash D, Faruq M, Lall H, Gogia H, Madan P, Kulkarni S, Chauhan H, Sengupta S, Kabra S, Indian SARS-CoV-2 Genomics Consortium (INSACOG)‡, Gupta RK, Singh SK, Agrawal A, Rakshit P, Nandicoori V, Tallapaka KB, Sowpati DT, Thangaraj K, Bashyam MD, Dalal A, Sivasubbu S, Scaria V, Parida A, Raghav SK, Prasad P, Sarin A, Mayor S, Ramakrishnan U, Palakodeti D, Seshasayee ASN, Bhat M, Shouche Y, Pillai A, Dikid T, Das S, Maitra A, Chinnaswamy S, Biswas NK, Desai AS, Pattabiraman C, Manjunatha MV, Mani RS, Udupi GA, Abraham P, Atul PV, Cherian SS. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science. 2021 17:1-382.
34. Shastri J, Parikh S, Agrawal S, Chatterjee N, Pathak M, Chaudhary S, Sharma C, Kanakan A, Vasudevan JS, Maurya R, Fatihi S, Thukral L, Agrawal A, Pinto L, Pandey R, Sunil S. Clinical, serological, whole genome sequence analyses to confirm SARS-CoV-2 reinfection in patients from Mumbai, India. Frontiers in Medicine 2021 8:215.
33. Klionsky ADJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, Abeliovich H, Abildgaard MH, Abudu YP, Acevedo-Arozena A, Adamopoulos IE, Adeli K, Adolph TE, Adornetto A, Aflaki E, Agam G, Agarwal A, Aggarwal BB, Agnello M, Agostinis P, Agrewala JV, Agrotis A, Aguilar PV, Ahmad ST, Ahmed ZM, Ahumada-Castro U, Aits S, Aizawa S, Akkoc Y, Akoumianaki T, Akpinar A, Al-Abd AM, Al-Akra L, Al-Gharaibeh A, Alaoui-Jamali MA, Alberti S, Alcocer-Gómez E, Alessandri C, Ali M, Al-Bari MAA, Aliwaini S, Alizadeh J, Almacellas E, Almasan A, Alonso A, Alonso GD, Altan-Bonnet N, Altieri DC, Álvarez ELC, Alves S, Costa CA, Alzaharna MA, Amadio M, Amantini C, Amaral C, Ambrosio S, Amer AO, Ammanathan V, An Z, Andersen SU, Andrabi SA, Andrade-Silva M, Andres AM, Angelini S, Ann D, Anozie UC, Ansari MY, Antas P, Antebi A, Antón Z, Anwar T, Apetoh L, Apostolova N, Araki T, Araki Y, Arasaki K, Araújo WL, Araya J, Arden C, Arévalo MA, Arguelles S, Arias E, Arikkath J, Arimoto H, Ariosa AR, Armstrong-James D, Arnauné-Pelloquin L, Aroca A, Arroyo DS, Arsov I, Artero R, Asaro DML, Aschner M, Ashrafizadeh M, Ashur-Fabian O, Atanasov AG, Au AK, Auberger P, Auner HW, Aurelian L, Autelli R, Avagliano L, Ávalos Y, Aveic S, Aveleira CA, Avin-Wittenberg T, Aydin Y, Ayton S, Ayyadevara S, Azzopardi M, Baba M, Backer JM, Backues SK, Bae D, Bae O, Bae SH, Baehrecke EH, Baek A, Baek S, Baek SH, Bagetta G, Bagniewska-Zadworna A, Bai H, Bai J, Bai X, Bai Y, Bairagi N, Baksi S, Balbi T, Baldari CT, Balduini W, Ballabio A, Ballester M, Balazadeh S, Balzan R, Bandopadhyay R, Banerjee S, Banerjee S, Bánréti A, Bao Y, Baptista MS, Baracca A, Barbati C, Bargiela A, Barilà D, Barlow PG, Barmada SJ, Barreiro E, Barreto GE, Bartek JE, Thukral L. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1. Autophagy. 2021 17:1-382.
32. MMeng B, Ferreira ATMI, Abdullahi A, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerba PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, Bowen JE, Joshi A, Walls AC, Jackson L, Cele S, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer K, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann S, Pizzuto M, Marco A, Corti D, Sigal A, James L, Veesler D, Hosmillo M, Lee JH, Sampaziotis F, Goodfellow IG, Matheson NJ, Thukral L, Sato K, Gupta RK, Kawabata R, Morizako N, Sadamasu K, Asakura H, Nagashima M, Yoshimura K, Ito J, Uriu K, Kosugi Y, Suganami M, Oide A, Yokoyama M, Chiba M, Butlertanaka EP, Tanaka YL, Motozono C, Nasser H, Shimizu R, Yuan Y, Kitazato K, Hasebe H, Nakagawa S, Wu J, Takahashi M, Fukuhara T, Shimizu K, Tsushima K, Kubo H, Kazuma Y, Nomura R, Horisawa Y, Nagata K, Kawai Y, Yanagida Y, Tashiro Y, Tokunaga K, Ozono S, Baker S, Dougan G, Hess C, Kingston N, Lehner PJ, Lyons PA, Owehand WH, Saunders C, Summers C, Thaventhiran JED, Toshner M, Weekes MP, Maxwell P, Shaw A, Bucke A, Calder J, Canna L, Domingo J, Elmer A, Fuller S, Harris J, Hewitt S, Kennet J, Jose S, Kourampa J, Meadows A, Brien CO, Price J, Publico C, Rastall R, Ribeiro C, Rowlands J, Ruffolo V, Tordesillas H, Bullman B, Dunmore BJ, Fawke S, Gräf S, Hodgson J, Huang C, Hunter K, Jones E, Legchenko E, Matara C, Martin J, Mescia L, O’Donnell C, Pointon L, Pond N, Shih J, Sutcliffe R, Tilly T, Treacy C, Tong Z, Wood J, Wylot M, Bergamaschi L, Betancourt A, Bower G. SARS-CoV-2 Omicron spike mediated immune escape and tropism shift (preprint). Web of Science. 2021 ID: ppcovidwho-331154.
31. Meng B, Ferreira IATM, Abdullahi A, Saito A, Kimura I, Yamasoba D, Kemp SA, Goonawardane N, Papa G, Fatihi S, Rathore S, Ikeda T, Toyoda M, Tan TS, Kuramochi J, Mitsunaga S, Ueno T, Charles OJ, CITIID-NIHR BioResource COVID-19 Collaboration, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Smith KGC, Bradley J, Choi J, Madissoon E, Meyer K, Mlcochova P, Doffinger R, Teichmann SA, James L, Lee JH, Thukral L, Sato K, Gupta RK. SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion. BioRxiv. 2021.
30. Paul S, Fatihi S, Sharma S, Kutum R, Fields R, Pant HC, Thukral L, Binukumar BK. CDK5 mediated phosphorylation of cytosolic phospholipase A2 regulates its activity and neuroinflammation in Parkinson’s Disease. BioRxiv. 2021 DOI: 10.1101/2021.11.05.467380.
29. Fatihi S, Rathore S, Pathak AK, Gahlot D, Mukerji M, Jatana N, Thukral L. OA rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Current Research in Structural Biology. 2021 3:290-300.
2020
28. Pathak AK, Fatihi S, Abbas T, Uppili B, Mishra GP, Ghosh A, Banu S, Bhoyar RC, Jain A, Divakar MK, Imran M, Faruq M, Sowpati DT, Raghav SK, Thukral LT, Mukerji M. Potential role of host-mediated RNA editing in intra-host variability of SARS-CoV-2 genomes. BioRxiv. 2020.
27. Pathak AK, Fatihi S, Abbas T, Uppili B, Mishra GP, Ghosh A, Banu S, Bhoyar RC, Jain A, Divakar MK, Imran M, Faruq M, Sowpati DT, Raghav SK, Thukral LT, Mukerji M. Intra-host variability in global SARS-CoV-2 genomes as signatures of RNA editing: implications in viral and host response outcomes. BioRxiv. 2020.
26. Shastri J, Parikh S, Agarwal S, Chatterjee N, Pathak M, Sharma C, Kanakan A, Vasudevan JS, Maurya R, Fatihi S, Thukral L, Agrawal A, Pinto L, Pandey R, Sunil S. Whole genome sequencing confirmed SARS-CoV-2 reinfections among healthcare workers in India with increased severity in the second episode. SSRN. 2020 DOI: 10.2139/ssrn.3688220.
25. Chua NK, Howe V, Jatana N, Hart-Smith G, Scott NA, Thukral L, Brown AJ. Squalene Monooxygenase at the Nexus between Cholesterol Homeostasis and Proteostasis. The FASEB Journal. 2020 34:1-1.
2019
24. Jatana N, Ascher DB, Pires DEV, Gokhale RS, Thukral L. IHuman LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations. Autophagy 2019, ,14:1-17.
23. TKumar S, Thakur J, Yadav K, Mitra M, Pal S, Ray A, Gupta S, Medatwal N, Gupta R, Mishra D, Rani P, Padhi S, Sharma P, Kapil Ar, Srivastava A, Priyakumar, U Deva, Dassgupta U, Thukral L, Bajaj A. Cholic Acid-Derived Amphiphile can Combat Gram-Positive Bacteria-mediated Infections via Disintegration of Lipid Clusters. CS Biomaterials Sci & Eng 2019, doi.org/10.1021/acsbiomaterials. 9b00706.
22. Grover R, Burse SA, Shankrit S, Aggarwal A, Kirty K, Narta K, Srivastav R, Ray AK, Malik G, Vats A, Motiani RK, Thukral L, Roy SS, Bhattacharya S, Sharma R, Natarajan K, Mukerji M, Pandey R, Gokhale RS, Natarajan VT;IMyg1 exonuclease couples the nuclear and mitochondrial translational programs through RNA processing. Nucleic Acids Res. 2019, 47(11):5852-5866.
21. Mitra M, Asad M, Kumar S, Yadav K, Chaudhary S, Bhavesh NS, Khalid S, Thukral L, Bajaj A. Distinct Intramolecular Hydrogen Bonding Dictates Antimicrobial Action of Membrane-Targeting Amphiphiles. J Phys Chem Lett. 2019, :754-760.
20. Yadav K, Kumar S, Mishra D, Asad M, Mitra M, Yavvari PS, Gupta S, Vedantham M, Ranga P, Komalla V, Pal S, Sharma P, Kapil A, Singh A, Singh N, Srivastava A, Thukral L, Bajaj A Deciphering the Role of Intramolecular Networking in Cholic Acid-Peptide Conjugates (CAPs) at Lipopolysaccharide Surface in Combating Gram-negative Bacterial Infections. J. Med. Chem. 2019, Doi:10.1021/acs.jmedchem.8b01357.
2018
19. Ray A, Ghosh A, Chakraborty R, Upadhyay SK, Maiti S, Sengupta S, Thukral L. Specific Cholesterol Binding Drives Drastic Structural Alterations in Apolipoprotein A1. J Phys Chem Lett. 2018,18;9(20):6060-6065.
18. Ray A, Grater F, Thukral L. Probing molecular forces in multi-component physiological membranes. Phys Chem Chem Phys. 2018, 20(4):, 2155-2161.
2017
17. Chua NK, Howe V, Jatana N, Thukral L, Brown AJ. A conserved degron containing an amphipathic helix regulates the cholesterol mediated turnover of human squalene monooxygenase, a rate-limiting enzyme in cholesterol synthesis. J Biol Chem. 2017, DOI: 10.1074/jbc.M117.794230.
16. Singh A, Gotherwal V, Junni P, Vijayan V, Tiwari M, Ganju P, Kumar A, Sharma P, Fatima T, Gupta A, Holla A, Kar HK, Khanna S, Thukral L, Malik G, Natarajan K, Gadgil CJ, Lahesmaa R, Natarajan VT, Rani R, Gokhale RS. Iapping architectural and transcriptional alterations in non-lesional and lesional epidermis in vitiligo. Sci Rep. 2018, DOI: 10.1038/s41598-017-10253-w.
15. Ramkumar A, Murthy D, Raja DA, Singh A, Krishnan A, Khanna S, Vats A, Thukral L, Sharma P, Sivasubbu S, Rani R, Natarajan VT, Gokhale RS. Classical autophagy proteins LC3B and ATG4B facilitate melanosome movement on cytoskeletal tracks. Autophagy 2017, 3, 13(8):1331-1347.
14. Ray A, Jatana N, Thukral L. Lipidated proteins: Spotlight on protein-membrane binding interfaces. Prog Biophys Mol Bio. 2017, DOI: 10.1016/j.pbiomolbio.
2016
13. Daidone I, Zanetti-Polzi L, Thukral L, Alekozai E, Amadei A. Theoretical-computational characterization of the temperature-dependent folding thermodynamics of a beta-hairpin peptide. Chem Phys Lett. 2016, 659:247-251.
12. Jatana N, Thukral L, Latha N. Structural signatures of DRD4 mutants revealed using molecular dynamics simulations: Implications for drug targeting. J Mol Model. 2016, 2, 22,1-14.
2015
11. Nagpal S, Tiwari S, Mapa K, Thukral L. Decoding structural properties of a partially unfolded protein substrate: en route to chaperone binding. PLoS Comput. Biol. 2015, 11(9):, e1004496.
10. Thukral L, Sengupta D, Ramkumar A, Murthy D, Agrawal N, Gokhale RS Molecular mechanism underlying recruitment and insertion of lipid-anchored LC3 proteins into membranes. Biophys J. 2015, 109(10):2067-78.
09. Srivastava S, Chaudhary S, Thukral L, Shi C, Gupta RD, Gupta R, Priyadarshan K, Vats A, Haque AS, Sankaranarayanan R, Natarajan VT, Sharma R, Aldrich CC, Gokhale RS. Unsaturated Lipid Assimilation by Mycobacteria Requires Auxiliary cis-trans Enoyl CoA Isomerase. Chem Biol. 2015, 17;22(12): 1577-87.
08. Thukral L, Schwarze S, Daidone I, Neuweiler H. Beta-structure within the denatured state of the helical protein domain BBL. J. Mol. Bio. 2015, 427(19): 3166-76.
07. Silla Y, Ray A, Thukral L, Sengupta S. Molecular Modeling indicates that homocysteine induces conformational changes in the structure of putative target proteins. J. Proteins and Proteomics. 2015, 6(3), 271-286.
06. Belardi, B.; Bertozzi, C. R. Structure and dynamics of DRD4 bound to an agonist and an antagonist using in silicoapproaches. Proteins. 2015, 83(5) 867-880.
05. Daidone I, Thukral L, Smith JC, Amadei A. SMonitoring the folding kinetics of a beta-hairpin by time-resolved IR spectroscopy in silico. J Phys Chem B. 2015. 119(14): 4849-56.
2013
04. Thukral L, Brown AJ. Lipid protein interactions in membranes: implications for health and diseases. Clin. Lipidol. 2013, 8(1), 43-45.
2011
03. Thukral L, Daidone I, Smith CJ. Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations. PLoS Comput. Biol. 2011, 7(9), e1002137.
02. Thukral L, Smith CJ, Daidone I. Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. J. Am. Chem. Soc. 2009, 131(50), 18147-18152.
2007
01. Thukral L, Shenoy S R, Bhushan Kumkum, Jayaram B. ProRegIn: A Regularity Index for the selection of native-like tertiary structures of proteins. Journal of Biosciences. 2007, 32(1), 71-81.