Neelanjan Mukherjee, PhD

Publications

• 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
• 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, Jagannathan S. Peptidyl-tRNA hydrolysis rate influences the efficiency of nonsense-mediated mRNA decay. bioRxiv. 2024 Jan 11. PubMed PMID: 38260612
• 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
• 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
• 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
• 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