Publications

Preprints:
Mamatharani DV, Purkayastha D., Niederwieser I., Rai S. K., Gaur P., Ganji M., Mukhopadhyay S., Voss T. S., Karmodiya K., The regulation of virulence gene expression is controlled by phase separation of heterochromatin protein 1 (HP1) in Plasmodium falciparum, Biorxiv, 2025

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, Biorxiv, 2025 [*equal contribution]

Peer-Reviewed Publications:

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 (just accepted)

Singh R. K., Swain P., Ganji M., Choubey S., Decoding the role of DNA sequence on protein-DNA co-condensation, PLoS Comp. Bio., 2025

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]

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]