Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Last Name
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Neelanjan Mukherjee

TitleAssistant Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BioChem&Molecular Genetics
Phone303/724-1623
    Other Positions
    TitleAssoc Director-Faculty
    InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
    DepartmentSOM-BioChem&Molecular Genetics


    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Walters K, Castro-Gutierrez R, Sarkar S, Baldwin A, Baker AS, Shilleh AH, Anderson AM, Nakayama M, Fugman T, Nakayasu ES, Mukherjee N, Russ HA. Proteogenomic Discovery of Novel Open Reading Frames With HLA Immune Presentation on Human ß-Cells. Diabetes. 2025 Sep 02. PMID: 40896833.
      View in: PubMed
    2. 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 02; 23(7):611-621. PMID: 40047825.
      View in: PubMed
    3. Purdy SC, Matlin K, Alderman C, Baldwin A, Shrivastava N, Dutta S, Webb KJ, Wolin A, Boulton DP, Kapali J, Landua JD, Lewis MT, Caino MC, Costello JC, Old W, Wang X, Zhao R, Ford HL, Mukherjee N. eIF3d and eIF3e mediate selective translational control of hypoxia that can be inhibited by novel small molecules. bioRxiv. 2025 May 29. PMID: 40501575.
      View in: PubMed
    4. 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 09; 5(7):100882. PMID: 40393459.
      View in: PubMed
    5. 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. PMID: 39928863.
      View in: PubMed
    6. 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 04; 13. PMID: 39630148.
      View in: PubMed
    7. 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. PMID: 38260612.
      View in: PubMed
    8. 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. PMID: 39327029.
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    9. Forman TE, Sajek MP, Larson ED, Mukherjee N, Fantauzzo KA. PDGFRa signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking. bioRxiv. 2024 Sep 16. PMID: 38617350.
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    10. 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. PMID: 39253515.
      View in: PubMed
    11. 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. PMID: 39091754.
      View in: PubMed
    12. 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 02; 7(12):bvad131. PMID: 37953901.
      View in: PubMed
    13. 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 10; 29(10):1458-1470. PMID: 37369529.
      View in: PubMed
    14. Wellman K, Fu R, Baldwin A, Rege J, Murphy E, Rainey WE, Mukherjee N. Transcriptomic Response Dynamics of Human Primary and Immortalized Adrenocortical Cells to Steroidogenic Stimuli. Cells. 2021 09 09; 10(9). PMID: 34572026.
      View in: PubMed
    15. Fu R, Wellman K, Baldwin A, Rege J, Walters K, Hirsekorn A, Riemondy K, E Rainey W, Mukherjee N. RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells. RNA. 2021 Jul 16; 27(8):933-945. PMID: 34074709.
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    16. 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. PMID: 34165268.
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    17. 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 05 25; 35(8):109178. PMID: 34038724.
      View in: PubMed
    18. Szczesniak MW, Wanowska E, Mukherjee N, Ohler U, Makalowska I. Towards a deeper annotation of human lncRNAs. Biochim Biophys Acta Gene Regul Mech. 2020 04; 1863(4):194385. PMID: 31128317.
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    19. Wessels HH, Lebedeva S, Hirsekorn A, Wurmus R, Akalin A, Mukherjee N, Ohler U. Global identification of functional microRNA-mRNA interactions in Drosophila. Nat Commun. 2019 04 09; 10(1):1626. PMID: 30967537.
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    20. 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 01 25; 47(2):570-581. PMID: 30517751.
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    21. Munteanu A, Mukherjee N, Ohler U. SSMART: sequence-structure motif identification for RNA-binding proteins. Bioinformatics. 2018 12 01; 34(23):3990-3998. PMID: 29893814.
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    22. 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 08; 27(8):1344-1359. PMID: 28596291.
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    23. 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 01; 24(1):86-96. PMID: 27870833.
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    24. 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. PMID: 26921342.
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    25. Wessels HH, Hirsekorn A, Ohler U, Mukherjee N. Identifying RBP Targets with RIP-seq. Methods Mol Biol. 2016; 1358:141-52. PMID: 26463382.
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    26. 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. PMID: 26657557.
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    27. 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. PMID: 24860013.
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    28. Mukherjee N, Jacobs NC, Hafner M, Kennington EA, Nusbaum JD, Tuschl T, Blackshear PJ, Ohler U. Global target mRNA specification and regulation by the RNA-binding protein ZFP36. Genome Biol. 2014 Jan 08; 15(1):R12. PMID: 24401661.
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    29. 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. PMID: 23816784.
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    30. 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. PMID: 23708386.
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    31. Ascano M, 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. PMID: 23235829.
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    32. 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. PMID: 22100165.
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    33. Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol. 2011 Aug 18; 12(8):R79. PMID: 21851591.
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    34. Mukherjee N, Corcoran DL, Nusbaum JD, Reid DW, Georgiev S, Hafner M, Ascano M, 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 05; 43(3):327-39. PMID: 21723170.
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    35. 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. 2010 Jul 23; 5(7):e11710. PMID: 20668518.
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    36. 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. PMID: 20836020.
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    37. 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. PMID: 19638969.
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    38. 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 01; 182(11):6779-88. PMID: 19454673.
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    39. 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. PMID: 18411299.
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    40. 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. PMID: 18075594.
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    41. 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. PMID: 23641147.
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    42. 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. PMID: 16200346.
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    43. 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 01; 64(3):293-302. PMID: 15754318.
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