Publications
- 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. Accepted Mol Cancer Res. 2025.
- Kolakada D, Fu R, Biziaev N, Shuvalov A, Lore M, Campbell AE, Cortázar MA, Sajek MP, Hesselberth JR, Mukherjee N, Alkalaeva E, Coban-Akdemir ZH, Jagannathan S. Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay. Cell Genom. 2025 Jul 9;5(7):100882. PubMed PMID: 40393459
- Walker ZJ, Vaeth KF, Baldwin A, Ohlstrom DJ, Reiman LT, Dennis 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 Jul 2;23(7):611-621. PubMed PMID: 40047825
- Walters K, Baldwin A, Liu Z, Larsen M, Mukherjee N, Kumar TR. Identification of FSH-regulated and estrous stage-specific transcriptional networks in mouse ovaries. Proc Natl Acad Sci U S A. 2025 Feb 18;122(7):e2411977122. PubMed PMID: 39928863
- Forman TE, Sajek MP, Larson ED, Mukherjee N, Fantauzzo KA. PDGFRa signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking. Elife. 2024 Dec 4;13. PubMed PMID: 39630148
- 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 Oct 29;34(10):1570-1581. PubMed PMID: 39327029
- 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. 2024 Aug 26. PubMed PMID: 39253515
- 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. 2024 Jul 24. PubMed PMID: 39091754
- Kolakada D, Fu R, Biziaev N, Shuvalov A, Lore M, Campbell AE, Cortázar MA, Sajek MP, Hesselberth JR, Mukherjee N, Alkalaeva E, Coban Akdemir ZH, Jagannathan S. Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay. bioRxiv. 2024 Nov 10. PubMed PMID: 38260612
- Kolakada D, Fu R, Biziaev N, Shuvalov A, Lore M, Campbell AE, Cortázar MA, Sajek MP, Hesselberth JR, Mukherjee N, Alkalaeva E, Jagannathan S. Peptidyl-tRNA hydrolysis rate influences the efficiency of nonsense-mediated mRNA decay. bioRxiv. 2024 Jan 11. PubMed PMID: 38260612
- Walters K, Sajek MP, Murphy E, Issaian A, Baldwin A, Harrison E, Daniels M, Reisz JA, 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 Oct;29(10):1458-1470. PubMed PMID: 37369529
- Fu R, Walters K, Kaufman ML, 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. J Endocr Soc. 2023 Nov 2;7(12):bvad131. PubMed PMID: 37953901
- Walters K, Sajek MP, Murphy E, Issaian A, Baldwin A, Harrison E, Daniels M, Reisz JA, 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 Oct;29(10):1458-1470. PubMed PMID: 37369529
- Fu R, Walters K, Kaufman ML, 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. J Endocr Soc. 2023 Nov 2;7(12):bvad131. PubMed PMID: 37953901
- Rothamel K, Arcos S, Kim B, Reasoner C, Lisy S, Mukherjee N, Ascano M. ELAVL1 primarily couples mRNA stability with the 3' UTRs of interferon-stimulated genes. Cell Rep. 2021 May 25;35(8):109178. PubMed PMID: 34038724
- Baldwin A, Morris AR, Mukherjee N. An Easy, Cost-Effective, and Scalable Method to Deplete Human Ribosomal RNA for RNA-seq. Curr Protoc. 2021 Jun;1(6):e176. PubMed PMID: 34165268
- Szczesniak MW, Wanowska E, Mukherjee N, Ohler U, Makalowska I. Towards a deeper annotation of human lncRNAs. Biochim Biophys Acta Gene Regul Mech. 2020 Apr;1863(4):194385. PubMed PMID: 31128317
- Mukherjee N, Wessels HH, Lebedeva S, Sajek M, Ghanbari M, Garzia A, Munteanu A, Yusuf D, Farazi T, Hoell JI, Akat KM, Akalin A, Tuschl T, Ohler U. Deciphering human ribonucleoprotein regulatory networks. Nucleic Acids Res. 2019 Jan 25;47(2):570-581. PubMed PMID: 30517751
- Munteanu A, Mukherjee N, Ohler U. SSMART: sequence-structure motif identification for RNA-binding proteins. Bioinformatics. 2018 Dec 1;34(23):3990-3998. PubMed PMID: 29893814
- Mukherjee N, Calviello L, Hirsekorn A, de Pretis S, Pelizzola M, Ohler U. Integrative classification of human coding and noncoding genes through RNA metabolism profiles. Nat Struct Mol Biol. 2017 Jan;24(1):86-96. PubMed PMID: 27870833
- Milek M, Imami K, Mukherjee N, Bortoli F, Zinnall U, Hazapis O, Trahan C, Oeffinger M, Heyd F, Ohler U, Selbach M, Landthaler M. DDX54 regulates transcriptome dynamics during DNA damage response. Genome Res. 2017 Aug;27(8):1344-1359. PubMed PMID: 28596291
- Huang YH, Peng W, Furuuchi N, Gerhart J, Rhodes K, Mukherjee N, Jimbo M, Gonye GE, Brody JR, Getts RC, Sawicki JA. Delivery of Therapeutics Targeting the mRNA-Binding Protein HuR Using 3DNA Nanocarriers Suppresses Ovarian Tumor Growth. Cancer Res. 2016 Mar 15;76(6):1549-59. PubMed PMID: 26921342
- Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U. Detecting actively translated open reading frames in ribosome profiling data. Nat Methods. 2016 Feb;13(2):165-70. PubMed PMID: 26657557
- Wessels HH, Hirsekorn A, Ohler U, Mukherjee N. Identifying RBP Targets with RIP-seq. Methods Mol Biol. 2016;1358:141-52. PubMed PMID: 26463382
- Farazi TA, Leonhardt 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 Jul;20(7):1090-102. PubMed PMID: 24860013
- Li S, Liberman LM, Mukherjee N, Benfey PN, Ohler U. Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Res. 2013 Oct;23(10):1730-9. PubMed PMID: 23816784
- 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 Methods. 2013 Jul;10(7):630-3. PubMed PMID: 23708386
- Ascano M Jr, Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, Corcoran DL, Langlois C, Munschauer M, Dewell S, Hafner M, Williams Z, Ohler U, Tuschl T. FMRP targets distinct mRNA sequence elements to regulate protein expression. Nature. 2012 Dec 20;492(7429):382-6. PubMed PMID: 23235829
- Gottwein E, Corcoran DL, Mukherjee N, Skalsky RL, Hafner M, Nusbaum JD, Shamulailatpam P, Love CL, Dave SS, Tuschl T, Ohler U, Cullen BR. Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host Microbe. 2011 Nov 17;10(5):515-26. PubMed PMID: 22100165
- 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 the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell. 2011 Aug 5;43(3):327-39. PubMed PMID: 21723170
- Morris AR, Mukherjee N, Keene JD. Systematic analysis of posttranscriptional gene expression. Wiley Interdiscip Rev Syst Biol Med. 2010 Mar-Apr;2(2):162-180. PubMed PMID: 20836020
- Papadaki O, Milatos S, Grammenoudi S, Mukherjee N, Keene JD, Kontoyiannis DL. Control of thymic T cell maturation, deletion and egress by the RNA-binding protein HuR. J Immunol. 2009 Jun 1;182(11):6779-88. PubMed PMID: 19454673
- Mukherjee N, Lager PJ, Friedersdorf MB, Thompson MA, Keene JD. Coordinated posttranscriptional mRNA population dynamics during T-cell activation. Mol Syst Biol. 2009;5:288. PubMed PMID: 19638969
- 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 Jun;28(12):4093-103. PubMed PMID: 18411299
- 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 Dec 13;450(7172):1096-9. PubMed PMID: 18075594
- 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. Transl Oncogenomics. 2007;2:99-105. PubMed PMID: 23641147
- 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 signaling pathway. J Neurooncol. 2006 Feb;76(3):227-37. PubMed PMID: 16200346
- 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. Prostate. 2005 Aug 1;64(3):293-302. PubMed PMID: 15754318