Shahu S., Baira S., Gupta S., Ganji M.
A DNA-binding protein senses DNA superhelicity to switch between bridging and nucleoprotein filament formation
Biorxiv, 2026
Hajra D., Mukherjee D., Vij R, Rajmani R., Dadireddy V., Das D., Hussain T., Ganji M., Tatu U., Chakravortty D.
Odoribacter splanchnicus mitigates Salmonella-induced gut inflammation and its associated pathogenesis via its secreted bacteriocin
Biorxiv, 2024
Banerjee A.*, Anand M.*, Srivastava M., Vidwath V. S., Ganji M.
High-Speed Multiplexed DNA-PAINT Imaging of Nuclear Organization Using an Expanded Sequence Repertoire
Nature Communications, 2026 [*equal contribution]
Mamatharani DV, Purkayastha D., Niederwieser I., Rai S. K., Gaur P., Ganji M., Mukhopadhyay S., Voss T. S., Karmodiya K.
Phase separation of heterochromatin protein 1 regulates virulence gene expression in Plasmodium falciparum
Cell Reports, 2026
Gaur P.*, Satheesh T.*, Singh K. R.*, Shahu S., Ramakrishnan S., Srivastava M., Neogi S., Choubey S.#, Ganji M.#
Sequence-dependent co-condensation of Lsr2 with DNA elucidates the mechanism of genome compaction in Mycobacterium tuberculosis
Nucleic Acids Research, 2025 [*equal contribution, #shared correspondence]
Mukherjee P., Alim Sk, Shahu S., Mondal S.,Chattopadhyay K., Ganji M., and Mazumder A.
Single-molecule experiments reveal NusG displaces transcription initiation factor σ⁷⁰ from mature elongation complexes
Nucleic Acids Research, 2025
Singh R. K., Swain P., Ganji M., Choubey S.
Decoding the role of DNA sequence on protein-DNA co-condensation
PLoS Comp. Bio., 2025
Banerjee A.*, Yadav S.*, Vidwath V. S.*, Kalita S., Agasti S., Joshi H.#, Ganji M.#
Proximity-based super-resolution imaging enabled by DNA base-stacking interactions
Small, 2025 [*equal contribution, #shared correspondence]
Chatterjee A., Roy A., Satheesh T., Das P., Mondal B., Kishore P., Ganji M., Dutta S
Structural insights into pre-pore intermediates of alpha-hemolysin in the lipidic environment
Nature Communications, 2025
Abbondanzieri E., et al.
Future Directions of the Prokaryotic Chromosome Field
Molecular Microbiology, 2025
Garg P., Satheesh T., Ganji M., Dutta S.
Cryo-EM reveals the mechanism of DNA compaction by Mycobacterium smegmatis Dps2
Journal of Molecular Biology, 2024
Shahu S., Vtyurina N., Das M., Meyer A., Ganji M.#, Abbondanzieri E.#
Bridging DNA contacts allow Dps from E. coli to condense DNA
Nucleic Acids Research, 2024 [#shared correspondence]
Unterauer E.M.*, Boushehri S.S.*, Jevdokimenko K.*, Masullo L.A., Ganji M., Idrissi S.S., Kowalewski R., Strauss S., Reinhardt S.C.M., Perovic A., Marr C., Opazo F., Fornasiero E.F., Jungmann R.
Spatial proteomics in neurons at single-protein resolution
Cell, 2024. [*equal contribution]
Mishra S., Jain D., Dey A. A., Nagaraja S., Srivastava M., Khatun O., Balamurugan K., Anand M., Tripathi S., Ganji M., Sannula K.
SARS-CoV-2 Nsp13 is a viral RHIM protein promoting cell death linked to Z-RNA sensing and ZBP1-RIPK3 signaling
iScience, Dec 2024
Banerjee A., Anand M., Kalita S., Ganji M.
Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures
Nature Nanotechnology, Aug 2023
Banerjee A.*, Anand M.*, Ganji M.
labeling approaches for DNA-paint super-resolution imaging
Nanoscale (Review), Mar 2023 [*equal contribution]
Before Joining IISc
Ganji M.*, Schlichthärle T*., Eklund A., Strauss S., Jungmann R.Quantitative assessment of labeling probes for super-resolution microscopy using designer DNA nanostructures, ChemPhysChem, Mar 2021 [*equal contribution]
Scheuder F., Unterauer E., Ganji M., Jungmann R., DNA-barcoded fluorescence microscopy for spatial omics, Proteomics (Review), Oct 2020. [Front Cover]
Eklund A.*, Ganji M.*, Gavins G., Seitz O., Jungmann R.,Peptide-PAINT Super-resolution imaging using transient coiled-coil interactions, Nano Letters, Aug 2020. [*equal contribution]
Elbatsh A.M.O., Kim E., Eeftens J.M., Raaijmakers J.A., Weide R.H.v.d., Bravo S., Ganji M., Bos J.u.d., Teunissen H., Medema R.H., Wit E.d., Haering C.H., Dekker C., Rowland B.D., Distinct Roles for Condensin’s Two ATPase Sites in Chromosome Condensation, Molecular Cell, Dec 2019.
Wade K.O.*, Wöhrstein J.B.*, Nickels P.C.*, Strauss S.*, Stehr F., Stein J., Schueder F., Strauss M.T., Ganji M., Schnitzbauer J., Grabmayr H., Yin P., Schwille P., Jungmann R. 124-Color Super-resolution Imaging by Engineering DNA-PAINT Blinking Kinetics, Nano Letters, 2019.
Covered by EurekaAlert, NanoWerk, Phys.Org, ScienceDaily, and many more
Schlichthärle T*., Ganji M.*, Auer A., Wade O. K., Jumgmann R. Bacterial-derived antibody binders as small adapters for DNA-PAINT microscopy, ChemBioChem, 2018.[*equal contribution]
Ganji M., Shaltiel I.A., Bisht S., Kim E., Kalichava A., Haering C.H., Dekker C. Real-time imaging of DNA loop extrusion by condensin, Science, 2018.
Covered by F1000prime, Physics.org, EurekaAlert, TheScientist, ScienceDaily, Discover, C&EN, LabManager, Newswise, and many more
Explanatory videos: Video-1, Video 2, Video 3, Video 4, PageFlow
Kim S.H.*, Ganji M.*, Kim E., Torre J.v.d., Abbondanzieri E., Dekker C. DNA sequence encodes the position of DNA supercoils, elife, 2018. [*equal contribution] [Biorxiv]
Ketterer P., Ananth A.N., Laman Trip D. S., Mishra A., Bertosin E., Ganji M., Torre J. V., Once P., Dietz H., Dekker C. DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex, Nature Communications, 2018.
Ganji M., Docter M., LeGrice S. F., Abbondanzieri E. DNA binding proteins explore multiple local configurations during docking via rapid rebinding, Nucleic Acids Research, 2016.
Ganji M.*, Kim S.H.*, Torre J.V., Abbondanzieri E., Dekker C. Intercalation-based single-molecule fluorescence assay to study DNA supercoil dynamics, Nano Letters, 2016. [*equal contribution]
Mahipal Ganji Lab 