Publications
Global identification of functional microRNA-mRNA interactions in Drosophila
Hans-Hermann Wessels, Svetlana Lebedeva, Antje Hirsekorn, Wurmus, Ricardo, Akalin, Altuna, Neelanjan Mukherjee, Uwe OhlerNature Communications 2019;
DOI
Towards a deeper annotation of human lncRNAs.
Michal Szczesniak, Wanowska, E., Neelanjan Mukherjee, Uwe Ohler, Makalowska, IzabelaBiochimica et biophysica acta. Gene regulatory mechanisms 2019;
DOI
PubMed
Deciphering human ribonucleoprotein regulatory networks
Neelanjan Mukherjee, Hans-Hermann Wessels, Svetlana Lebedeva, Sajek, Marcin, Mahsa Ghanbari, Garzia, Aitor, Alina-Cristina Munteanu, Yusuf, Dilmurat, Farazi, Thalia, Hoell, Jessica I., Akat, Kemal M., Akalin, Altuna, Tuschl, Thomas, Uwe OhlerNucleic Acids Research 2018;
DOI
SSMART: sequence-structure motif identification for RNA-binding proteins.
Alina-Cristina Munteanu, Neelanjan Mukherjee, Uwe OhlerDOI
PubMed
Integrative classification of human coding and noncoding genes through RNA metabolism profiles
Neelanjan Mukherjee, Lorenzo Calviello, Antje Hirsekorn, de Pretis, S., Pelizzola, M., Uwe OhlerNat. Struct. Mol. Biol. 2017;
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PubMed
DDX54 regulates transcriptome dynamics during DNA damage response
Milek, M., Imami, K., Neelanjan Mukherjee, Bortoli, F., Zinnall, U., Hazapis, O., Trahan, C., Oeffinger, M., Heyd, F., Uwe Ohler, Selbach, M., Landthaler, M.Genome Res. 2017;
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PubMed
Detecting actively translated open reading frames in ribosome profiling data
Lorenzo Calviello, Neelanjan Mukherjee, Wyler, Emanuel, Zauber, Henrik, Antje Hirsekorn, Selbach, Matthias, Landthaler, Markus, Obermayer, Benedikt, Uwe OhlerNature Methods 2016;
DOI
PubMed
Identifying RBP Targets with RIP-seq
Hans-Hermann Wessels, Antje Hirsekorn, Uwe Ohler, Neelanjan MukherjeeMethods Mol. Biol. 2016;
DOI
PubMed
Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets
Farazi, T. A., Leonhardt, C. S., Neelanjan Mukherjee, Mihailovic, A., Li, S., Max, K. E., Meyer, C., Yamaji, M., Cekan, P., Nicholas Charles Jacobs, Gerstberger, S., Bognanni, C., Larsson, E., Uwe Ohler, Tuschl, T.RNA 2014;
DOI
PubMed
Global target mRNA specification and regulation by the RNA-binding protein ZFP36
Neelanjan Mukherjee, Nicholas Charles Jacobs, Hafner, M., Kennington, E. A., Nusbaum, J. D., Tuschl, T., Blackshear, P. J., Uwe OhlerGenome Biol. 2014;
DOI
PubMed
Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
Li, S., Liberman, L. M., Neelanjan Mukherjee, Benfey, P. N., Uwe OhlerPubMed Central
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PubMed
MicroRNA target site identification by integrating sequence and binding information
Majoros, W. H., Lekprasert, P., Neelanjan Mukherjee, Skalsky, R. L., Corcoran, D. L., Cullen, B. R., Uwe OhlerNat. Methods 2013;
PubMed Central
DOI
PubMed
FMRP targets distinct mRNA sequence elements to regulate protein expression
Ascano, M., Neelanjan Mukherjee, Bandaru, P., Miller, J. B., Nusbaum, J. D., Corcoran, D. L., Langlois, C., Munschauer, M., Dewell, S., Hafner, M., Williams, Z., Uwe Ohler, Tuschl, T.Nature 2012;
PubMed Central
DOI
PubMed
Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines
Gottwein, E., Corcoran, D. L., Neelanjan Mukherjee, Skalsky, R. L., Hafner, M., Nusbaum, J. D., Shamulailatpam, P., Love, C. L., Dave, S. S., Tuschl, T., Uwe Ohler, Cullen, B. R.Cell Host Microbe 2011;
PubMed Central
DOI
PubMed
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data
Corcoran, D. L., Georgiev, S., Neelanjan Mukherjee, Gottwein, E., Skalsky, R. L., Keene, J. D., Uwe OhlerGenome Biol. 2011;
PubMed Central
DOI
PubMed
Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability
Neelanjan Mukherjee, Corcoran, D. L., Nusbaum, J. D., Reid, D. W., Georgiev, S., Hafner, M., Ascano, M., Tuschl, T., Uwe Ohler, Keene, J. D.Mol. Cell 2011;
PubMed Central
DOI
PubMed
Systematic analysis of posttranscriptional gene expression
Morris, A. R., Neelanjan Mukherjee, Keene, J. D.Wiley Interdiscip Rev Syst Biol Med 2010;
Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs
Neplioueva, V., Dobrikova, E. Y., Neelanjan Mukherjee, Keene, J. D., Gromeier, M.PLoS ONE 2010;
Coordinated posttranscriptional mRNA population dynamics during T-cell activation
Neelanjan Mukherjee, Lager, P. J., Friedersdorf, M. B., Thompson, M. A., Keene, J. D.Mol. Syst. Biol. 2009;
Control of thymic T cell maturation, deletion and egress by the RNA-binding protein HuR
Papadaki, O., Milatos, S., Grammenoudi, S., Neelanjan Mukherjee, Keene, J. D., Kontoyiannis, D. L.J. Immunol. 2009;
Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets
Morris, A. R., Neelanjan Mukherjee, Keene, J. D.Mol. Cell. Biol. 2008;
A viral microRNA functions as an orthologue of cellular miR-155
Gottwein, E., Neelanjan Mukherjee, Sachse, C., Frenzel, C., Majoros, W. H., Chi, J. T., Braich, R., Manoharan, M., Soutschek, J., Uwe Ohler, Cullen, B. R.Nature 2007;
PubMed Central
DOI
PubMed
A STAT3 Gene Expression Signature in Gliomas is Associated with a Poor Prognosis
Alvarez, J. V., Neelanjan Mukherjee, Chakravarti, A., Robe, P., Zhai, G., Chakladar, A., Loeffler, J., Black, P., Frank, D. A.Transl Oncogenomics 2007;
Radiation enhances the invasive potential of primary glioblastoma cells via activation of the Rho signaling pathway
Zhai, G. G., Malhotra, R., Delaney, M., Latham, D., Nestler, U., Zhang, M., Neelanjan Mukherjee, Song, Q., Robe, P., Chakravarti, A.J. Neurooncol. 2006;
Adenovirus-mediated inhibition of survivin expression sensitizes human prostate cancer cells to paclitaxel in vitro and in vivo
Zhang, M., Neelanjan Mukherjee, Bermudez, R. S., Latham, D. E., Delaney, M. A., Zietman, A. L., Shipley, W. U., Chakravarti, A.Prostate 2005;