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 Sep 9;10(9). PubMed PMID: 34572026
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
Fu R, Wellman K, Baldwin A, Rege J, Walters K, Hirsekorn A, Riemondy K, Rainey WE, Mukherjee N. RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells. RNA. 2021 Jun 1. [Epub ahead of print] PubMed PMID: 34074709
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
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
Szczesniak MW, Wanowska E, Mukherjee N, Ohler U, Makalowska I. Towards a deeper annotation of human lncRNAs. Biochim Biophys Acta Gene Regul Mech. 2019 May 22. [Epub ahead of print] PubMed PMID: 31128317
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 Apr 9;10(1):1626. PubMed PMID: 30967537
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, 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. 2018 Dec 5. [Epub ahead of print] PubMed PMID: 30517751
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
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