Publications

2018

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 (Accepted)

Wessels HH, Hirsekorn A, Mukherjee N, Ohler U. Global identification of functional microRNA::mRNA interactions in Drosophila. Nature Communications (In revision).

 

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

 

 
2017


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.


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.

 

 
2016


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.


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

 

 
2015

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.

 

 
2014

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.

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.

2013

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


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.

 

 

2012


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.

 

 

 

2011


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.

 

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.

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.

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.

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

 

2009

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

 

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.
 

 

2008


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.


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.

 

 

2007


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.

 
2006

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.

 

2005


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.


*Co-first Author, #Corresponding Author