2025
Bhattacharyya C, Subramanian K, Uppili B, Biswas NK, Ramdas S, Tallapaka KBharadwaj, Arvind P, Rupanagudi KValli, Maitra A, Nagabandi T et al..
2025. Mapping genetic diversity with the GenomeIndia project.. Nat Genet. 57(4):767-773.
2024
Mishra S, Bansal M, Prasad V, Singh VPartap, Murthy S, Parmar S, Utescher T, Khangar R.
2024. Did the Deccan Volcanism impact the Indian flora during the Maastrichtian? EARTH-SCIENCE REVIEWS. 258(104950)
Tanaka S, Matsushita Y, Hanaki Y, Higaki T, Kamamoto N, Matsushita K, Higashiyama T, Fujimoto K, Ueda M.
2024. HD-ZIP IV genes are essential for embryo initial cell polarization and the radial axis formation in Arabidopsis.. Curr Biol.
Liu X, Zhang Y, Wen Z, Hao Y, Banks CAS, Cesare J, Bhattacharya S, Arvindekar S, Lange JJ, Xie Y et al..
2024. An integrated structural model of the DNA damage-responsive H3K4me3 binding WDR76:SPIN1 complex with the nucleosome.. Proc Natl Acad Sci U S A. 121(33):e2318601121.
Varma A, Udupa S, Sengupta M, Ghosh PKumar, Thirumalai V.
2024. A machine-learning tool to identify bistable states from calcium imaging data.. J Physiol.
Mohanakrishnan V, Sivaraj KK, Jeong H-W, Bovay E, Dharmalingam B, M Bixel G, Dinh VVuong, Petkova M, Ugarte IParedes, Kuo Y-T et al..
2024. Specialized post-arterial capillaries facilitate adult bone remodelling.. Nat Cell Biol.
2023
Kikuchi DW, Allen WL, Arbuckle K, Aubier TG, Briolat ES, Burdfield-Steel ER, Cheney KL, Daňková K, Elias M, Hämäläinen L et al..
2023. The evolution and ecology of multiple antipredator defences.. J Evol Biol.
Devi MR, Ummalyma SB, Brockmann A, Raina V, Rajashekar Y.
2023. Nutritional properties of giant water bug, a traditional edible insect species of North-East India.. Bioengineered. 14(1):2252669.
2022
Uddin A, Malla JA, Kumar H, Kumari M, Sinha S, Sharma VK, Kumar Y, Talukdar P, Lahiri M, Maiti TK et al..
2022. Development of a Systematic Strategy toward Promotion of α-Synuclein Aggregation Using 2-Hydroxyisophthalamide-Based Systems. . Biochemistry.
Bhattacharjee R, Udgaonkar JB.
2022. Differentiating between the sequence of structural events on alternative pathways of folding of a heterodimeric protein.. Protein Sci. :e4513.
Urban L, De Niz M, Fernández-Chiappe F, Ebrahimi H, Han LKM, Mehta D, Mencia R, Mittal D, Ochola E, Quezada CPaz et al..
2022. eLife's new model and its impact on science communication.. Elife. 11
Kumar H, Udgaonkar JB.
2022. Elongation of Fibrils Formed by a Tau Fragment is Inhibited by a Transient Dimeric Intermediate.. J Phys Chem B.
Pal S., Udgaonkar JB.
2022. Evolutionarily conserved proline residues impede the misfolding of the mouse prion protein by destabilizing an aggregation-competent partially unfolded form . J Mol Biol..
Bhatia S, Udgaonkar JB.
2022. Heterogeneity in Protein Folding and Unfolding Reactions.. Chem Rev.
Malhotra P, Udgaonkar JB.
2022. Native State Hydrogen Exchange-Mass Spectrometry Methods to Probe Protein Folding and Unfolding.. Methods Mol Biol. 2376:143-159.
Ullanat V, Kasukurthi N, Viswanath S.
2022. PrISM: Precision for Integrative Structural Models. Bioinformatics.
Kent BA, Holman C, Amoako E, Antonietti A, Azam JM, Ballhausen H, Bediako Y, Belasen AM, Carneiro CFD, Chen Y-C et al..
2022. Recommendations for empowering early career researchers to improve research culture and practice.. PLoS Biol. 20(7):e3001680.
2021
Bhate SH, Udgaonkar JB, Das R.
2021. Destabilization of polar interactions in the prion protein triggers misfolding and oligomerization.. Protein Sci.
Srivastava T, Kumar A, Kumar V, Umapathy G.
2021. Diet Drives Differences in Reproductive Synchrony in Two Sympatric Mountain Ungulates in the Himalaya. FRONTIERS IN ECOLOGY AND EVOLUTION. 9(647465)
Unnikrishnan S, Gadagkar R.
2021. Dominance behaviour and division of labour in the tropical primitively eusocial wasp Ropalidia cyathiformis. INSECTES SOCIAUX.
Chakravarthy A, Nandakumar A, George G, Ranganathan S, Umashankar S, Shettigar N, Palakodeti D, Gulyani A, Ramesh A.
2021. Engineered RNA biosensors enable ultrasensitive SARS-CoV-2 detection in a simple color and luminescence assay.. Life Sci Alliance. 4(12)
Vilizzi L, Copp GH, Hill JE, Adamovich B, Aislabie L, Akin D, Al-Faisal AJ, Almeida D, Azmai MNAmal, Bakiu R et al..
2021. A global-scale screening of non-native aquatic organisms to identify potentially invasive species under current and future climate conditions.. Sci Total Environ. 788:147868.
Vilizzi L, Copp GH, Hill JE, Adamovich B, Aislabie L, Akin D, Al-Faisal AJ, Almeida D, Azmai MNAmal, Bakiu R et al..
2021. A global-scale screening of non-native aquatic organisms to identify potentially invasive species under current and future climate conditions.. Sci Total Environ. 788:147868.
Wills C, Wang B, Fang S, Wang Y, Jin Y, Lutz J, Thompson J, Harms KE, Pulla S, Pasion B et al..
2021. Interactions between all pairs of neighboring trees in 16 forests worldwide reveal details of unique ecological processes in each forest, and provide windows into their evolutionary histories.. PLoS Comput Biol. 17(4):e1008853.
Kumar H, Udgaonkar JB.
2021. The Lys 280 ➔ Gln mutation mimicking disease-linked acetylation of Lys 280 in tau extends the structural core of fibrils and modulates their catalytic properties.. Protein Sci.
Bhatia S, Krishnamoorthy G, Udgaonkar JB.
2021. Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein.. J Am Chem Soc.
Sen S, Kumar H, Udgaonkar JB.
2021. Microsecond dynamics during the binding-induced folding of an intrinsically disordered protein.. J Mol Biol. :167254.
Bhatia S, Krishnamoorthy G, Udgaonkar JB.
2021. Resolving Site-Specific Heterogeneity of the Unfolded State under Folding Conditions.. J Phys Chem Lett. :3295-3302.
Prabhakara C, Godbole R, Sil P, Jahnavi S, Gulzar S-E-J, van Zanten TS, Sheth D, Subhash N, Chandra A, Shivaraj A et al..
2021. Strategies to target SARS-CoV-2 entry and infection using dual mechanisms of inhibition by acidification inhibitors.. PLoS Pathog. 17(7):e1009706.
2020
Rheinbay E, Nielsen MMuhlig, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RIstrup, Lin Z et al..
2020. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.. Nature. 578(7793):102-111.
Rheinbay E, Nielsen MMuhlig, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RIstrup, Lin Z et al..
2020. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.. Nature. 578(7793):102-111.
K Shafi M, Joshi AG, Meenakshi I, Pasha SNaseer, Harini K, Mahita J, Sajeevan RSivarajan, Karpe SD, Ghosh P, Nitish S et al..
2020. Dataset for the combined transcriptome assembly of and functional annotation.. Data Brief. 30:105416.
Mukherjee A, Singh R, Udayan S, Biswas S, Reddy PPurushotha, Manmadhan S, George G, Kumar S, Das R, Rao BM et al..
2020. A Fyn biosensor reveals pulsatile, spatially localized kinase activity and signaling crosstalk in live mammalian cells.. Elife. 9
Salian SRaj, Pandya RKirit, Laxminarayana SLakshmi Ko, Krishnamurthy H, Cheredath A, Tholeti P, Uppangala S, Kalthur G, Majumdar S, Schlatt S et al..
2020. Impact of Temperature and Time Interval Prior to Immature Testicular-Tissue Organotypic Culture on Cellular Niche.. Reprod Sci.
Joshi AG, Harini K, Meenakshi I, K Shafi M, Pasha SNaseer, Mahita J, Sajeevan RSivarajan, Karpe SD, Ghosh P, Nitish S et al..
2020. A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways.. MethodsX. 7:101053.
McClanahan TR, Maina JM, Darling ES, Guillaume MM, Muthiga N, D’agata S, Leblond J, Arthur R, Jupiter SD, Wilson S et al..
2020. Large geographic variability in the resistance of corals to thermal stress. Global Ecology and Biogeography.
Pasha SNaseer, K Shafi M, Joshi AG, Meenakshi I, Harini K, Mahita J, Sajeevan RSivarajan, Karpe SD, Ghosh P, Nitish S et al..
2020. The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera).. Genomics. 112(1):621-628.
2019
Sen S, Udgaonkar JB.
2019. Binding-induced folding under unfolding conditions: Switching between induced fit and conformational selection mechanisms.. J Biol Chem. 294(45):16942-16952.
Caputi L, Carradec Q, Eveillard D, Kirilovsky A, Pelletier E, Karlusich J, Vieira FRocha Jime, Villar E(, Chaffron S, Malviya S et al..
2019. Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems. GLOBAL BIOGEOCHEMICAL CYCLES. 33(3):391-419.
Nandwani N, Surana P, Negi H, Mascarenhas NM, Udgaonkar JB, Das R, Gosavi S.
2019. A five-residue motif for the design of domain swapping in proteins.. Nat Commun. 10(1):452.
Upadhyay AKumar, Sowdhamini R.
2019. Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: .. Bioinform Biol Insights. 13:1177932218821362.
Udgaonkar JB.
2019. Introducing the Mechanical Forces in Biochemistry Special Issue.. Biochemistry. 58(47):4655-4656.
Kumar H, Udgaonkar JB.
2019. Mechanistic approaches to understand the prion-like propagation of aggregates of the human tau protein.. Biochim Biophys Acta Proteins Proteom. 1867(10):922-932.
Goluguri RReddy, Sen S, Udgaonkar J.
2019. Microsecond sub-domain motions and the folding and misfolding of the mouse prion protein.. Elife. 8
Sengupta I, Udgaonkar J.
2019. Monitoring site-specific conformational changes in real-time reveals a misfolding mechanism of the prion protein.. Elife. 8
Upadhyay N, Kar D, Mahajan BDeepak, Nanda S, Rahiman R, Panchakshari NAbhay, Bhagavatula L, Datta S.
2019. The multitasking abilities of MATE transporters in plants.. J Exp Bot.
Bhatia S, Krishnamoorthy G, Dhar D, Udgaonkar JB.
2019. Observation of Continuous Contraction and a Metastable Misfolded State during the Collapse and Folding of a Small Protein.. J Mol Biol.
Cyriac VP, Johny A, Umesh P, Palot M, Campbell PD.
2019. Rediscovery of Cnemaspis nilagirica Manamendra-Arachchi, Batuwita and Pethiyagoda, 2007 (Squamata: Gekkonidae) from Kerala, India with notes on morphology and distribution. ZOOTAXA. 4586(1):98-108.
Pranatharthi A, Thomas P, Udayashankar AH, Bhavani C, Suresh SBangalore, Krishna S, Thatte J, Srikantia N, Ross CR, Srivastava S.
2019. RhoC regulates radioresistance via crosstalk of ROCK2 with the DNA repair machinery in cervical cancer.. J Exp Clin Cancer Res. 38(1):392.
Moulick R, Goluguri RReddy, Udgaonkar JB.
2019. Ruggedness in the Free Energy Landscape Dictates Misfolding of the Prion Protein.. J Mol Biol.
McClanahan TR, Darling ES, Maina JM, Muthiga NA, D'agata S, Jupiter SD, Arthur R, Wilson SK, Mangubhai S, Nand Y et al..
2019. Temperature patterns and mechanisms influencing coral bleaching during the 2016 El Nino. Nature Climate Change. 9:845–851.
2018
Khan I, Prakash A, Issar S, Umarani M, Sasidharan R, Masagalli JN, Lama P, Venkatesan R, Agashe D.
2018. Female Density-Dependent Chemical Warfare Underlies Fitness Effects of Group Sex Ratio in Flour Beetles. American Naturalist.
Ashwini N, Sajeevan RSivarajan, Udayakumar M, Nataraja KN.
2018. Identification of splice variant of in ssp. genotypes under salinity stress.. 3 Biotech. 8(8):345.
Amanullah A, Mishra R, Upadhyay A, Reddy PP, Das R, Mishra A.
2018. Indomethacin elicits proteasomal dysfunctions develops apoptosis through mitochondrial abnormalities.. J Cell Physiol. 233(2):1685-1699.
Kalappa DMonnanda, Subramani PAnnamalai, Basavanna SKanchanaha, Ghosh SKumar, Sundaramurthy V, Uragayala S, Tiwari S, Anvikar AR, Valecha N.
2018. Influence of midgut microbiota in Anopheles stephensi on Plasmodium berghei infections.. Malar J. 17(1):385.
Sabareesan AThody, Mathew MK, Udgaonkar JB.
2018. Mechanism of aggregation and membrane interactions of mammalian prion protein.. Biochim Biophys Acta.
Kumar H, Udgaonkar JB.
2018. Mechanistic and Structural Origins of the Asymmetric Barrier to Prion-like Cross-Seeding between Tau-3R and Tau-4R.. J Mol Biol.
Jethva PN, Udgaonkar JB.
2018. The Osmolyte TMAO Modulates Protein Folding Cooperativity by Altering Global Protein Stability.. Biochemistry.
Vijayakrishnan S, Kumar MAnanda, Umapathy G, Kumar V, Sinha A.
2018. Physiological stress responses in wild Asian elephants Elephas maximus in a human-dominated landscape in the Western Ghats, southern India.. Gen Comp Endocrinol. 266:150-156.
Saha P, Nandi AK, Unnikrishnan S, Shilpa MC, Shukla SP, Mandal S, Mitra A, Gadagkar R.
2018. A Route to Direct Fitness: Natural and Experimentally Induced Queen Succession in the Tropical Primitively Eusocial Wasp Ropalidia marginata . JOURNAL OF INSECT BEHAVIOR . 31(1):54-65.
Bhatia S, Krishnamoorthy G, Udgaonkar JB.
2018. Site-specific time-resolved FRET reveals local variations in the unfolding mechanism in an apparently two-state protein unfolding transition.. Phys Chem Chem Phys. 20(5):3216-3232.
Sengupta I, Udgaonkar JB.
2018. Structural mechanisms of oligomer and amyloid fibril formation by the prion protein.. Chem Commun (Camb).
2017
Nandwani N, Surana P, Udgaonkar JB, Das R, Gosavi S.
2017. Amino-acid composition after loop deletion drives domain swapping.. Protein Sci. 26(10)
Malhotra P, Jethva PN, Udgaonkar JB.
2017. Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding.. Biochemistry. 56(31):4053-4063.
Sen S, Goluguri RReddy, Udgaonkar JB.
2017. A Dry Transition State More Compact Than the Native State Is Stabilized by Non-Native Interactions during the Unfolding of a Small Protein.. Biochemistry.
Sengupta I, Udgaonkar JB.
2017. Expression and purification of single cysteine-containing mutant variants of the mouse prion protein by oxidative refolding.. Protein Expr Purif.
Thutupalli S, Uppaluri S, Constable GWA, Levin SA, Stone HA, Tarnita CE, Brangwynne CP.
2017. Farming and public goods production in Caenorhabditis elegans populations.. Proc Natl Acad Sci U S A. 114(9):2289-2294.
Sabareesan AThody, Udgaonkar JB.
2017. The G126V Mutation in the Mouse Prion Protein Hinders Nucleation-Dependent Fibril Formation by Slowing Initial Fibril Growth and by Increasing the Critical Concentration.. Biochemistry. 56(44):5931-5942.
Moulick R, Udgaonkar JB.
2017. Identification and structural characterization of the precursor conformation of the prion protein which directly initiates misfolding and oligomerization.. J Mol Biol.
Jethva PN, Udgaonkar JB.
2017. Modulation of the Extent of Cooperative Structural Change During Protein Folding by Chemical Denaturant.. J Phys Chem B. 121(35):8263-8275.
Kumar H, Singh J, Kumari P, Udgaonkar JB.
2017. Modulation of the extent of structural heterogeneity in α-synuclein fibrils by the small molecule thioflavin T.. J Biol Chem.
Adurthi S, Kumar MM, Vinodkumar HS, Mukherjee G, Krishnamurthy H, K Acharya K, Bafna UD, Uma DK, Abhishekh B, Krishna S et al..
2017. Oestrogen Receptor-α binds the FOXP3 promoter and modulates regulatory T-cell function in human cervical cancer.. Sci Rep. 7(1):17289.
Sengupta I, Bhate SH, Das R, Udgaonkar JB.
2017. Salt-mediated oligomerization of the mouse prion protein monitored by real time NMR.. J Mol Biol.
Aghera N, Udgaonkar JB.
2017. Stepwise Assembly of β-Sheet Structure during the Folding of an SH3 Domain Revealed by a Pulsed Hydrogen Exchange Mass Spectrometry Study.. Biochemistry.
Hilgen G, Sorbaro M, Pirmoradian S, Muthmann J-O, Kepiro IEdit, Ullo S, Ramirez CJuarez, Encinas APuente, Maccione A, Berdondini L et al..
2017. Unsupervised Spike Sorting for Large-Scale, High-Density Multielectrode Arrays.. Cell Rep. 18(10):2521-2532.
2016
Nussinov R, Udgaonkar JB.
2016. Editorial overview: Folding and binding: Dynamic conformational heterogeneity is pivotal to cell life.. Curr Opin Struct Biol. 36:iv-vi.
Upadhyay AKumar, Sowdhamini R.
2016. Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information.. PLoS One. 11(7):e0159627.
Malhotra P, Udgaonkar JB.
2016. How cooperative are protein folding and unfolding transitions? Protein Sci.
Goluguri RReddy, Udgaonkar JB.
2016. Microsecond rearrangements of hydrophobic clusters in an initially collapsed globule prime structure formation during the folding of a small protein.. J Mol Biol.
Mondal S, Kallianpur MV, Udgaonkar JB, Krishnamoorthy G.
2016. Molecular crowding causes narrowing of population heterogeneity and restricts internal dynamics in a protein. METHODS AND APPLICATIONS IN FLUORESCENCE. 4(1)
Mithileshwari C, Srivastava T, Kumar V, Kumar A, Umapathy G.
2016. Non-invasive assessment of fecal progestagens and pregnancy detection in Himalayan musk deer (Moschus chrysogaster).. Theriogenology. 85(2):216-23.
Sabareesan AThody, Singh J, Roy S, Udgaonkar JB, Mathew MK.
2016. The Pathogenic A116V Mutation Enhances Ion-Selective Channel Formation by Prion Protein in Membranes.. Biophys J. 110(8):1766-76.
Singh J, Udgaonkar JB.
2016. The pathogenic mutation T182A converts the prion protein into a molten globule-like conformation whose misfolding to oligomers but not to fibrils is drastically accelerated.. Biochemistry. 55(3):459-69.
Sabareesan AT, Udgaonkar JB.
2016. Pathogenic mutations within the disordered palindromic region of the prion protein induce structure therein and accelerate the formation of misfolded oligomers.. J Mol Biol.
Malhotra P, Udgaonkar JB.
2016. Secondary Structural Change Can Occur Diffusely and Not Modularly during Protein Folding and Unfolding Reactions.. J Am Chem Soc. 138(18):5866-78.
D'Souza F, Pudakalakatti SM, Uppangala S, Honguntikar S, Salian SRaj, Kalthur G, Pasricha R, Appajigowda D, Atreya HS, Adiga SKumar.
2016. Unraveling the association between genetic integrity and metabolic activity in pre-implantation stage embryos.. Sci Rep. 6:37291.
Singh J, Udgaonkar JB.
2016. Unraveling the Molecular Mechanism of pH-Induced Misfolding and Oligomerization of the Prion Protein.. J Mol Biol. 428(6):1345-55.
2015
Shingate P, Upadhyay A, Khader S, Sowdhamini R.
2015. 172 Computational analysis and prediction of proteins that undergo domain swapping.. J Biomol Struct Dyn. 33 Suppl 1:112-3.
Milán-Garcés EA, Thaore P, Udgaonkar JB, Puranik M.
2015. Formation of a CH-π contact in the core of native barstar during folding.. J Phys Chem B. 119(7):2928-32.
Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N et al..
2015. Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties.. BMC Plant Biol. 15:212.
Singh J, Udgaonkar JB.
2015. Molecular Mechanism of the Misfolding and Oligomerization of the Prion Protein: Current Understanding and Its Implications.. Biochemistry. 54(29):4431-42.
Moulick R, Das R, Udgaonkar JB.
2015. Partially Unfolded Forms of the Prion Protein Populated under Misfolding-promoting Conditions: CHARACTERIZATION BY HYDROGEN EXCHANGE MASS SPECTROMETRY AND NMR.. J Biol Chem. 290(42):25227-40.
Goluguri RReddy, Udgaonkar JB.
2015. Rise of the Helix from a Collapsed Globule during the Folding of Monellin.. Biochemistry. 54(34):5356-65.
Singh J, Udgaonkar JB.
2015. Structural effects of multiple pathogenic mutations suggest a model for the initiation of misfolding of the prion protein.. Angew Chem Int Ed Engl. 54(26):7529-33.
Malhotra P, Udgaonkar JB.
2015. Tuning Cooperativity on the Free Energy Landscape of Protein Folding.. Biochemistry. 54(22):3431-41.