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Our landmark paper demonstrating siPOOL proof-of-concept data
 

Hannus M. et. al.: siPools: highly complex but accurately defined siRNA pools eliminate off-target effects. Nucleic Acids Res 42(12): 8049-61(2014) 
 

Publications citing riboPOOLs


Goar et al. (2022) Molecular Connectivity between Extracytoplasmic Sigma Factors and PhoP Accounts for Coupled Mycobacterial Stress Response Journal of Bacteriology

Pastor et al. (2022) Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea Biomolecules

 Wahl et al. (2022) Comparison of rRNA depletion methods for efcient bacterial mRNA sequencing Scientific Reports

Wittekind et al. (2022) The novel protein ScrA acts through the SaeRS two component system to regulate virulence gene expression in Staphylococcus aureus Molecular Microbiology

Fujii et al. (2022) Ribotype-dependent growth inhibition and promotion by erythritol in Cutibacterium acnes Journal of Cosmetic Dermatology

Weihua Qin et. Al (2022) Probing protein ubiquitination in live cells bioRxiv - preprint

Puiggené, Ò. et al. (2022) Extracellular degradation of a polyurethane oligomer involving outer membrane vesicles and further insights on the degradation of 2,4-diaminotoluene in Pseudomonas capeferrum TDA1 Scientific Reports

M. A. Lawlo et al. (2021) A transposon expression burst accompanies the activation of Y-chromosome fertility genes during Drosophila spermatogenesis Nature Communications

Felix Grünberger et al. (2021) Nanopore sequencing of RNA and cDNA molecules in Escherichia coli RNA

Martin Gélinas et al. (2021) The de novo Purine Biosynthesis Pathway Is the Only Commonly Regulated Cellular Pathway during Biofilm Formation in TSBBased Medium in Staphylococcus aureus and Enterococcus faecalis Microbiology Spectrum

Weipeng Mo et al. (2021) Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing Genome Biology

Dimitar Plamenov Petrov et al. (2021) Quantitative  profiling  and  dynamics  of  mRNA  modifications  in  Escherichia coli

Bhat et al. (2021) Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome Science

Mio Takeuchi, Hideyoshi Yoshioka (2021) Acetate excretion by a methanotroph, Methylocaldum marinum S8, under aerobic conditions Bioscience, Biotechnology, and Biochemistry

Blaze et al (2021) Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior Nature Communications

Y. Long (2021) FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing Nature Protocols

Neil Fleck & Christoph Grundner (2021) A Cas12a-based CRISPR interference system for multigene regulation in mycobacteria JBC

J. Andersen et al (2021) Identification of small molecules that interfere with c-di-GMP signaling and induce dispersal of Pseudomonas aeruginosa biofilms npj Biofilms and Microbiomes

La Rosa et al (2021) Compensatory evolution of Pseudomonas aeruginosa’s slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis Nature Communications 

Fuchs et al (2021) Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach PLOS Genetics

Martin Benda (2020) PhD dissertation A possible functional link between RNA degradation and transcription in Bacillus subtilis

Ryan. D et. al (2020) A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gutmicrobe Bacteroides thetaiotaomicron. Nature Communications 

Kim, I et. al (2019) Efficient depletion of ribosomal RNA for RNA sequencing in planarians. BMC Genomics 

Galmozzi, C. V. et. al (2019) Selective ribosome profiling to study interactions of translating ribosomes in yeast. Nature Protocols 
 

Publications citing raPOOLs


Nötzold, L. et. al The long non-coding RNA LINC00152 is essential for cell cycle progression through mitosis in HeLa cells. Scientific Reports 7, 2265 (2017)  Also cites siPOOL
 

Publications citing siPOOLs


Dessauges et al. (2022) Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics Molecular Systems Biology

Falke et al. (2022) Knockdown of the stem cell marker Musashi-1 inhibits endometrial cancer growth and sensitizes cells to radiation Stem Cell Research & Therapy

Gutierrez-Prat et al. (2022) DUSP4 protects BRAF- and NRAS-mutant melanoma from oncogene overdose through modulation of MITF Life Science Alliance

Lechner et al. (2022) Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target Nature Chemical Biology

Daniel Kummer et al. (2022)  A JAM-A–tetraspanin–αvβ5 integrin complex regulates contact inhibition of locomotion Journal of Cell Biology

Delicato, A. et al (2022) YB-1 Oncoprotein Controls PI3K/Akt Pathway by Reducing Pten Protein Level Genes

Szachnowski et al. (2022) Transcriptomic landscapes of SARS-CoV-2-infected and bystander lung cells reveal a selective upregulation of NF-κB-dependent coding and non-coding proviral transcripts bioRxiv - preprint

Hauffe, L. et al. (2022) Eukaryotic translation initiation factor 4E binding protein 1 (EIF4EBP1) expression in glioblastoma is driven by ETS1- and MYBL2-dependent transcriptional activation Cell Death Discovery

Till Braun et al.  (2022) Non-canonical function of AGO2 augments T-cell receptor signaling in T-cell prolymphocytic leukemia Amercian Association for Cancer Research

Karabid et al.  (2022) Angpt2/Tie2 autostimulatory loop controls tumorigenesis EMBO Mol Med

Kerstin Dörner et al. (2022) Genome-wide RNAi screen identifies novel players in human 60S subunit biogenesis including key enzymes of polyamine metabolism Nucleic Acids Research

X. Li et al.  (2022) 5’isomiR-183-5p|+2 Elicits Tumor Suppressor Activity in a Negative Feedback Loop with E2F1  Journal of Experimental & Clinical Cancer Research - preprint - 

Thölmann et al. (2022) JAM-A interacts with α3β1 integrin and tetraspanins CD151 and CD9 to regulate collective cell migration of polarized epithelial cells Cellular and Molecular Life Sciences

Thea Reinkens et al. (2021) Ago-RIP Sequencing Identifies New MicroRNA-449a-5p  Target Genes Increasing Sorafenib Efficacy in  Hepatocellular Carcinoma Journal Of Cancer

Belitškin et al. (2021) Hepsin regulates TGFβ signaling via fibronectin proteolysis EMBO reports

Q. Zou et al (2021) Utility of single-shot compressed sensing cardiac magnetic resonance cine imaging for assessment of biventricular function in free-breathing and arrhythmic pediatric patients International Journal of Cardiology

J. Laisney et al (2021) Delivery of short hairpin RNA in the neotropical brown stink bug, Euschistus heros, using a composite nanomaterial Pesticide Biochemistry and Physiology

Indacochea et al (2021) Cold-inducible RNA bindi ng protein promotes breast cancer cell maligna ncy by regulating Cys tatin C levels Cold Spring Harbor Laboratory Press

Khan et al (2021) Developing Tumor Radiosensitivity Signatures Using LncRNAs Radiation Research

Ghodke et al (2021) AHNAK controls 53BP1-mediated p53 response by restraining 53BP1 oligomerization and phase separation Molecular Cell

Gaza et al (2021) Identification of novel targets of miR-622 in hepatocellular carcinoma reveals common regulation of cooperating genes and outlines the oncogenic role of zinc finger CCHC-type containing 11 Neoplasia

Indacochea et al (2021) Cold-inducible RNA binding protein promotes breast cancer cell maligna ncy by regulating Cys tatin C levels Cold Spring Harbor Laboratory Press

Mercier et al (2020) Endosomal membrane tension regulates ESCRT-III-dependent intra-lumenal vesicle formation Nature Cell Biology

Ghosh et al (2020) Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation The EMBO Journal 
 
Dhamija et. al (2020) A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation Nature Cell Biology

Gandhi et. al (2020) The lncRNA lincNMR regulates nucleotide metabolism via a YBX1 - RRM2 axis in cancer Nature Communications 

Stephan et. al (2020) MICOS assembly controls mitochondrial inner membrane remodeling and crista junction redistribution to mediate cristae formation The EMBO journal 

Liebig et. al (2020) HuRdling Senescence: HuR Breaks BRAF-Induced Senescence in Melanocytes and Supports Melanoma Growth. MDPI Cancers 

Prasad et. al (2020) The UPR sensor IRE1α and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections. Nature Communications 

Marchetto et. al (2020)  Oncogenic hijacking of a developmental transcription factor evokes vulnerability toward oxidative stress in Ewing sarcoma. Nature Communications 

Larios, J. et. al (2020) ALIX- and ESCRT-III–dependent sorting of tetraspanins to exosomes. JCB 

Mahli, A. et. al (2019) Bone Morphogenic Protein-8B Expression is Induced in Steatotic Hepatocytes and Promotes Hepatic Steatosis and Inflammation in Vitro. Cells 

Renner, K. et. al (2019) Restricting Glycolysis Preserves T Cell Effector Functions and Augments Checkpoint Therapy. Cell Rep 

Werner, S. et. al (2019) MRTF-A controls myofibroblastic differentiation of human multipotent stromal cells and their tumour-supporting function in xenograft models. Scientific Reports 

Braun, C. et. al (2019) Inhibition of peptidyl-prolyl isomerase (PIN1) and BRAF signaling to target melanoma. Am J Transl Res

Kappelmann-Fenzl, M. et. al (2019) C-Jun drives melanoma progression in PTEN wild type melanoma cells. Cell Death Dis 

Simchovitz, A et. al (2019) NEAT1 is overexpressed in Parkinson’s disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. FASEB J 

Mahli, A et. al (2019) Bone Morphogenetic Protein-8B Expression is Induced in Steatotic Hepatocytes and Promotes Hepatic Steatosis and Inflammation In Vitro. Cells 

Dietrich, P et. al (2019) The Delta Subunit of Rod-Specific Photoreceptor cGMP Phosphodiesterase (PDE6D) Contributes to Hepatocellular Carcinoma Progression. Cancers 

Feuerer, L et. al (2019) Role of MIA (melanoma inhibitory activity) in melanocyte senescence. Pigment Cell Melanoma Res 

Ziegler, C. et. al (2019) The long non‐coding RNA LINC00941 and SPRR5 are novel regulators of human epidermal homeostasis. EMBO Rep 

Choi, K. et. al (2019) Binary Targeting of siRNA to Hematologic Cancer Cells In Vivo Using Layer‐by‐Layer Nanoparticles. Adv Funct Mater 

Spies, J. et. al (2019) 53BP1 nuclear bodies enforce replication timing at under-replicated DNA to limit heritable DNA damage. Nat Cell Biol 

Dietrich, P. et al. (2019) Neuroblastoma RAS Viral Oncogene Homolog (NRAS) Is a Novel Prognostic Marker and Contributes to Sorafenib Resistance in Hepatocellular Carcinoma. Neoplasia 

Vendramin, R. et al. (2018) SAMMSON fosters cancer cell fitness by concertedly enhancing mitochondrial and cytosolic translation. Nat Struct Mol Biol 

Coscia, F. et al. (2018) Multi-level Proteomics Identifies CT45 as a Chemosensitivity Mediator and Immunotherapy Target in Ovarian Cancer. Cell 

Kästle, M. et al. FKBP51 modulates steroid sensitivity and NFκB signalling: A novel anti-inflammatory drug target. Eur J Immunol 

Stieglitz, D. et al. BMP6-induced modulation of the tumor micro-milieu. Oncogene 10.1038/s41388-018-0475-x (2018)

Weber, A., Schwarz, S. C. et al. Epigenome-wide DNA methylation profiling in Progressive Supranuclear Palsy reveals major changes at DLX1. Nat Commun 9, 2929 (2018) 

Noethel, B. et al. Transition of responsive mechanosensitive elements from focal adhesions to adherens junctions upon epithelial differentiation. Mol Biol Cell 10.1091/mbc.E17-06-0387(2018) 

Prestigiacomo, V., and Suter-Dick, L.  Nrf2 protects stellate cells from Smad-dependent cell activation. PLoS One 13, e0201044 (2018)

Vallin, B. et al. Novel short isoforms of adenylyl cyclase as negative regulators of cAMP production. Biochim Biophys Acta - Mol Cell Res 1865: 1326–1340 (2018) 

Rietscher, K. et al.14-3-3 Proteins Regulate Desmosomal Adhesion via Plakophilins.” Journal of cell science 131(10). (2018).

Jiang, P. et al. Genome-Scale Signatures of Gene Interaction from Compound Screens Predict Clinical Efficacy of Targeted Cancer Therapies.” Cell Systems 6(3): 343–354.e5.  (2018).

So, D. et al. Cervical Cancer Is Addicted to SIRT1 Disarming the AIM2 Antiviral Defense. Oncogene (2018).

Klingenberg, M. et al. The lncRNA CASC9 and RNA Binding Protein HNRNPL Form a Complex and Co-Regulate Genes Linked to AKT Signaling. Hepatology (2018).

Polycarpou-Schwarz, M. et al. The Cancer-Associated Microprotein CASIMO1 Controls Cell Proliferation and Interacts with Squalene Epoxidase Modulating Lipid Droplet Formation. Oncogene (2018) 

Zeiner, P. S. et al. CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival. Acta Neuropathol. Commun. 6, 18 (2018).

Ziegelmann, B et al. Lithium chloride effectively kills the honey bee parasite Varroa destructor by a systemic mode of action. Scientific Reports 8(1), 683 (2018) 

Dietrich, P. et al. Wild type Kirsten rat sarcoma is a novel microRNA-622-regulated therapeutic target for hepatocellular carcinoma and contributes to sorafenib resistance. Gut (2017) 

Dietrich, P. et al. Wild-type KRAS is a novel therapeutic target for melanoma contributing to primary and acquired resistance to BRAF inhibition. Oncogene (2017) 

Kaller, M. et al. Loss of p53-inducible long non-coding RNA LINC01021 increases chemosensitivity. Oncotarget 8, 102783–102800 (2017).

Ilina, E. I. et al. Effects of soluble CPE on glioma cell migration are associated with mTOR activation and enhanced glucose flux. Oncotarget 8, 67567–67591 (2017).

Goyal, A. et al. A cautionary tale of sense-antisense gene pairs: independent regulation despite inverse correlation of expression. Nucleic Acids Research (2017) http://dx.doi.org/10.1093/nar/gkx952

Steinbach, A. et al. ERAP1 overexpression in HPV-induced malignancies: A possible novel immune evasion mechanism. Oncoimmunology 6, e1336594 (2017).

Sluch, V. M. et al. Enhanced Stem Cell Differentiation and Immunopurification of Genome Engineered Human Retinal Ganglion Cells. STEM CELLS Translational Medicine. (2017) doi:10.1002/sctm.17-0059

Armento, A. et al. Carboxypeptidase E transmits its anti-migratory function in glioma cells via transcriptional regulation of cell architecture and motility regulating factors. International Journal of Oncology 51(2), 702-714 (2017)

Nötzold, L. et al. The long non-coding RNA LINC00152 is essential for cell cycle progression through mitosis in HeLa cells. Scientific Reports 7, 2265 (2017)  Also cites raPOOL

Welsbie, D. S. et al. Enhanced Functional Genomic Screening Identifies Novel Mediators of Dual Leucine Zipper Kinase-Dependent Injury Signaling in Neurons. Neuron 94(6), 1142–1154.e6 (2017)

Ruivo, M. T. G. et al. Host AMPK Is a Modulator of Plasmodium Liver Infection. Cell Rep. 1–7 (2017). 

Treiber, T. et al. A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis. Mol. Cell 66, 270–284.e13 (2017).

Seiler, J. et al. The lncRNA VELUCT strongly regulates viability of lung cancer cells despite its extremely low abundance. Nucleic Acids Res. (2017) 

Goyal, A. et al. Challenges of CRISPR/Cas9 applications for long non-coding RNA genes Nucleic Acids Res. (2016)

Ott, C. A. et al. Induction of exportin-5 expression during melanoma development supports the cellular behavior of human malignant melanoma cells. Oncotarget 7, 62292–62304 (2016).

Adriaens, C. et al. p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. Nat. Med. (2016). 

Coll-Bonfill, N. et al. Slug is increased in vascular remodeling and induces a smooth muscle cell proliferative phenotype. PLoS One 11, 1–21 (2016).

Kordaß, T. et al. SOX5 is involved in balanced MITF regulation in human melanoma cells. BMC Med. Genomics 9, 10 (2016).

Hauptmann, J. et al. Biochemical isolation of Argonaute protein complexes by Ago-APP. Proc. Natl. Acad. Sci. 112, 11841–11845 (2015).

Blirando, K. et al. The stellate vascular smooth muscle cell phenotype is induced by IL-1β via the secretion of PGE2 and subsequent cAMP-dependent protein kinase A activation. Biochim. Biophys. Acta. 1853, 3235–3247 (2015).

Tuncay, H. et al. JAM-A regulates cortical dynein localization through Cdc42 to control planar spindle orientation during mitosis. Nat. Commun. 6, 8128 (2015).

Schraivogel, D. et al. Importin-β facilitates nuclear import of human GW proteins and balances cytoplasmic gene silencing protein levels. Nucleic Acids Res. (2015)

Schönemann L. et al.: Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33. Genes Dev. 28(21), 2381-93 (2014)

Prasad, V. et al. Chemical induction of unfolded protein response enhances cancer cell killing through lytic virus infection. J. Virol. 88, 13086–13098 (2014).

Patrick C.H. Lo, PhD: siRNAs: Jumping in the Pool to Avoid Hitting Innocent Bystanders. BioTechniques (2014)

Thalyana S. Advances in RNAi Tools and Technologies. Genetic Engineering & Biotechnology News. April 33(8): 20-22, 24 (2013) 
 


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