Publications

*Co-first Author, #Corresponding Author

Pre-prints

Walters K*, Guiterrez RC*, Sakhar S, Baldwin A,. Nakayasu ES, Mukherjee N#, Russ HA#. Proteogenomic discovery of novel and regulatory open reading frames in human beta cells. In revision.

White LK, Dobson K, Del Pozo S, Bilodeaux JM, Andersen SE, Baldwin A, Barrington C, Körtel N, Martinez-Seidel F, Strugar SM, Watt KEN, Mukherjee N, Hesselberth JR. Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing. bioRxiv.

Lo J, Vaeth KF, Bhardwaj G, Mukherjee N, Russ HA, Moore JK, Taliaferro JM. The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites. bioRxiv.

Kolakada D, Fu R, Biziaev N, Shuvalov A, Lore M, Campbell AE, Cortázar MA, Sajek MP, Hesselberth JR, Mukherjee N, Alkalaeva E, Jagannathan S. Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay efficiency. bioRxiv.

Peer-reviewed

Walker ZJ, Vaeth KF, Baldwin A, Ohlstrom DJ, Reiman LT, Denns KA, Matlin K, Idler BM, Stevens BM, Mukherjee N#, Sherbenou DW#. Ribosome Profiling Reveals Translational Reprogramming via mTOR Activation in Omacetaxine Resistant Multiple Myeloma. Mol Cancer Res. 2025.

Walters K, Baldwin A, Liu Z, Larsen M, Mukherjee N#, Kumar TR#. Discovery of FSH-regulated and estrous stage-specific transcriptional networks in mouse ovaries. PNAS 2025.

Sajek MP, Bilodeau DY, Beer MA, Horton E, Miyamoto Y, Velle KB, Eckmann L, Fritz-Laylin L, Rissland OS#, Mukherjee N#. Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists. Genome Res 2024.

Forman TE, Sajek MP, Larson ED, Mukherjee N, Fantauzzo KA.. PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking. Elife 2024.

Fu R, Kaufman ML, Walters K, Koc K, Baldwin A, Clay MR, Basham KJ, Kiseljak-Vassiliades K#, Fishbein L#, Mukherjee N#. In situ spatial reconstruction of distinct normal and pathological cell populations within the human adrenal gland. Journal of the Endocrine Society 2023.

Walters K, Sajek MP, Issaian A, Baldwin A, Harrison E, Murphy E, Daniels M, Haines J, Hansen K, D’Alessandro A, Mukherjee N. Small-molecule Ro-08-2750 interacts with many RNA-binding proteins and elicits MUSASHI2-independent phenotypes. RNA 2023.

Fu R*, Wellman K*, Baldwin A, Rege J, Walthers K, Riemondy K, Rainey WR, Mukherjee N. RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells. RNA 2021.

Wellman K*, Fu R*, Baldwin A, Rege J, Murphy E, Rainey WR, Mukherjee N. Transcriptomic Response Dynamics of Human Primary and Immortalized Adrenocortical Cells to Steroidogenic Stimuli. Cells 2021.

Rothamel KL, Arcos SE, Kim B, Reasoner C, Lisy S, Mukherjee N, Ascano M. ELAVL1 Primarily Couples mRNA Stabilitywith the 3'UTRs of Interferon Stimulated Genes. Cell Reports 2021.

Baldwin A, Morris AR, Mukherjee N. An easy, cost-effective, and scalable method to deplete human ribosomal RNA for RNA-seq. Current Protocols 2021.

Szcześniak MW, Wanowska E, Mukherjee N, Ohler U, Makałowska I. Towards a deeper annotation of human lncRNAs. Biochim Biophys Acta Gene Regul Mech 2020.

Mukherjee N, Wessels HH, Lebedeva S, Sajek M, Garzia A, Ghanbari M, Munteanu A, Farazi T, Yusuf D, Spitzer J, Akat K, Akalin A, Tuschl T, Ohler U. Deciphering human ribonucleoprotein regulatory networks. Nucleic Acids Research 2019.

Wessels HH, Lebedeva S, Hirsekorn A, Wurmus R, Akalin A, Mukherjee N, Ohler U. Global identification of functional microRNA::mRNA interactions in Drosophila. Nature Communications 2019.

Munteanu A, Mukherjee N, Ohler U. SSMART: Sequence-structure motif identification for RNA-binding proteins. Bioinformatics 2018.

Milek M, Imami K, Mukherjee N, de Bortoli F, Zinnall U, Hazapis O, Heyd F, Ohler U, Selbach M, Landthaler M. DDX54 regulates transcriptome dynamics during DNA damage response. Genome Research 2017.

Mukherjee N#, Calviello L, Hirsekkorn A, de Pretis S, Pellizola M, Ohler U#. Integrative classification of human coding and non-coding genes based on RNA metabolism profiles. Nat Struct Mol Biol 2017.

News and Views: Bedova-Reina OC, Ponting CP. Functional RNA classes: a matter of time? Nat Struct Mol Biol.

Huang Y, Peng W, Furuuchi N, Gerhart J, Rhodes K, Mukherjee N, Jimbo M, Gonye GE, Brody JR, Getts RC, Sawicki JA. Targeted inhibition of the mRNA-binding protein HuR suppresses ovarian tumor growth. Cancer Research 2017.

Wessels HH, Hirsekorn A, Ohler U, Mukherjee N#. Identifying RBP Targets with RIP-seq. Methods Mol Biol 2017.

Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U. A spectral analysis approach to detect actively translated open reading frames in high-resolution ribosome profiling data. Nat Meth 2015.

News and Views: Baranov PV, Michel AM. Illuminating translation with ribosome profiling spectra. Nat Meth.

Mukherjee N#, Jacobs NJ, Hafner M, Kennington EA, Nusbaum JD, Tuschl T, Blackshear PJ, Ohler U#. Global target mRNA specification and regulation by RNA-Binding Protein ZFP36. Genome Biology 2014.

Editorial: Attar N. The RBPome: where the brain meets the brawn. Genome Biology.

Farazi T, Leonard CS, Mukherjee N, Mihailovic A, Li S, Max KE, Meyer C, Yamaji M, Cekan P, Jacobs NC, Gerstberger S, Bognanni C, Larsson E, Ohler U, Tuschl T. Identification of the RNA Recognition Element of the RBPMS Family of RNA-Binding Proteins and their Transcriptome-Wide mRNA Targets. RNA 2014.

Li S, Liberman LM, Mukherjee N, Benfey PN, Ohler U. Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Research 2013.

Majoros WH, Lekprasert P, Mukherjee N, Skalsky RL, Corcoran DL, Cullen BR, Ohler U. MicroRNA target site identification by integrating sequence and binding information. Nat Meth 2013.

Ascano M, Mukherjee N, Bandaru P, Miller JB, Nusbaum J, Corcoran D, Langlois C, Munschauer M, Hafner M, Williams Z, Ohler U, Tuschl T. FMR1 targets distinct mRNA sequence elements to regulate protein expression. Nature 2012.

News and Views: Jayaseelan S and Tenebaum SA. Neurodevelopmental disorders: Signalling pathways of fragile X syndrome. Nature.

Gottwein E, Corcoran DL, Mukherjee N, Skalsky RL, Hafner M, Nusbaum JD, Shamulailatpam P, Love CL, Dave SS, Tuschl T, Ohler U, Cullen BR. microRNA targetome analysis of latently KSHV-infected primary effusion lymphoma cell lines using PAR-CLIP. Cell Host Microbe 2011.

Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U. Definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol 2011.

Mukherjee N, Corcoran DL, Nusbaum JD, Reid DW, Georgiev S,Hafner M, Ascano M Jr, Tuschl T, Ohler U, Keene JD. Integrative regulatory mapping indicates that RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell 2011.

Preview: Srikantan S, Gorospe M. UneCLIPsing HuR Nuclear Function. Mol Cell.

Neplioueva V, Dobrikova EY, Mukherjee N, Keene JD, Gromeier M. Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs. PLoS ONE 2011.

Morris AR, Mukherjee N, Keene JD. Systematic analysis of posttranscriptional gene expression. Wiley Interdiscip Rev Syst Biol Med 2011.

Mukherjee N, Lager PJ, Friedersdorf MB, Thompson MA, Keene JD. Coordinated posttranscriptional mRNA population dynamics during T-cell activation. Mol Syst Biol 2009.

News and Views: Gorospe M. Ribonucleoprotein dynamics connects mRNA networks with drug mechanisms. Mol Syst Biol.
Spotlight: Gordon E. The Dynamics of Post-transcription. ACS Chemical Biology.

Papadaki O, Milatos S, Grammenoudi S, Mukherjee N, Keene JD, Kontoyiannis DL. Control of thymic T cell
maturation, deletion and egress bythe RNA-binding protein HuR. J Immunol 2009.

Morris AR, Mukherjee N, Keene JD. Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets. Mol Cell Biol 2008.

Gottwein E, Mukherjee N, Sachse C, Frenzel C, Majoros WH, Chi JT, Braich R, Manoharan M, Soutschek J, Ohler U, Cullen BR. A viral microRNA functions as an orthologue of cellular miR-155. Nature 2008.

Alvarez JV, Mukherjee N, Chakravarti A, Robe P, Zhai G, Chakladar A, Loeffler J, Black P, Frank DA. A STAT3 Gene Expression Signature in Gliomas is Associated with a Poor Prognosis. Translational Oncogenomics 2007.

Zhai GG, Malhotra R, Delaney M, Latham D, Nestler U, Zhang M, Mukherjee N, Song Q, Robe P, Chakravarti A. Radiation enhances the invasive potential of primary glioblastoma cells via activation of the Rho signalling pathway. J Neurooncol 2006.

Zhang M, Mukherjee N*, Bermudez RS, Latham DE, Delaney MA, Zietman AL, Shipley WU, Chakravarti A. Adenovirus-mediated inhibition of survivin expression sensitizes human prostate cancer cells to paclitaxel in vitro and in vivo. The Prostate 2005.