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
Zhou et al. (2023) Coupling of co-transcriptional splicing and 3’ end Pol II pausing during termination in Arabidopsis
Genome Biology
Ahmed et al. (2023) Benzene Amide Ether Scaffold is Active against Non-replicating and Intracellular
Mycobacterium tuberculosis ACS Infectious diseases
Müller et al. (2023) Mechanisms of readthrough mitigation reveal principles of GCN1-mediated translational quality control
Cell
Abada et al. (2023) Aerobic bacteria produce nitric oxide via denitrification and promote algal population collapse
The ISME Journal
Al-Jourani et al. (2023) Identification of D-arabinan-degrading enzymes in mycobacteria
Nature communications
Hadjeras et al. (2023) Unraveling the small proteome of the plant symbiont
Sinorhizobium meliloti by ribosome profiling and proteogenomics
microLife
Li et al. (2023) Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation
Nature Communications
Hadjeras et al. (2023) Revealing the small proteome of
Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry
microLife
Matiasek et al. (2023) Mystery of fatal ‘staggering disease’ unravelled: novel rustrela virus causes severe meningoencephalomyelitis in domestic cats
Nature communications
Steiner et al. (2023) Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of
Neisseria gonorrhoeae mBio
Sahonero-Canavesi et al. (2022) Disentangling the lipid divide: Identification of key enzymes for the biosynthesis of membrane-spanning and ether lipids in Bacteria
Science Advances
Zhang et al. (2022) A simple and robust method for isolating and analyzing chromatin-bound RNAs in Arabidopsis
Plant Methods
Palomar-Siles et al. (2022) Translational readthrough of nonsense mutant TP53 by mRNA incorporation of 5-Fluorouridine
Cell Death & Disease
Snieckute et al. (2022) Ribosome stalling is a signal for metabolic regulation by the ribotoxic stress response
Cell Metabolism
Parris et al. (2022) Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry
Journal of Veterinary Diagnostic Investigation
Kim et al. (2022) Characterization of an Entner–Doudoroff pathway-activated
Escherichia coli Biotechnology for Biofuels and Bioproducts
Cannon et al. (2022) Multi-site fungicides suppress banana Panama disease, caused by
Fusarium oxysporum f. sp.
cubense Tropical Race 4
PLOS Pathogens
Fernández-Justel et al. (2022) Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner
Cell Reports
Meindl et al. (2022) A rapid protocol for ribosome profiling of low input samples
bioRxiv also cites siFractor
Li et al. (2022) Sensing of individual stalled 80S ribosomes by Fap1 for nonfunctional rRNA turnover
Molecular Cell
Fritz et al. (2022) Transcriptomic fingerprint of bacterial infection in lower extremity ulcers
APMIS
Chen et al. (2022) Protocol for affordable and efficient profiling of nascent RNAs in bread wheat using GRO-seq
STAR Protocols
Jia et al. (2022) An atlas of plant full-length RNA reveals tissue-specific and monocots–dicots conserved regulation of poly(A) tail length
Nature Plants
Alarcón-Schumacher et al. (2022) Isolation of a virus causing a chronic infection in the archaeal model organism
Haloferax volcanii reveals antiviral activities of a provirus
PNAS
Waditee‑Sirisattha et al. (2022) Global transcriptional and circadian regulation in a halotolerant cyanobacterium Halothece sp. PCC7418
Scientific Reports
Jung et al. (2022) Opportunities and challenges to profile mRNA modifications in Escherichia coli
ChemBioChem
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 efficient 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
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. Lawlor 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
Denolly et al. (2023) Dengue virus NS1 secretion is regulated via importin-subunit β1 controlling expression of the chaperone GRp78 and targeted by the clinical drug ivermectin
mBio
Heydasch et al. (2023) GTPase activating protein DLC1 spatio-temporally regulates Rho signaling
eLife
Haiduk et al. (2023) Dysregulated Stem Cell Markers Musashi-1 and Musashi-2 are Associated with Therapy Resistance in Inflammatory Breast Cancer
Archives of Medical Research
Sommer et al. (2023) Expression of Bone Morphogenetic Protein 14 in Liver Disease and Cancer
MDPI
Rübsam et al. (2023) Polarity signaling balances epithelial contractility and mechanical resistance S
cientific Reports
Deng et al. (2023)
Cryptosporidium uses CSpV1 to activate host type I interferon and attenuate antiparasitic defenses
Nature Communications
Zimmermann et al. (2023) Cold Atmospheric Plasma Triggers Apoptosis via the Unfolded Protein Response in Melanoma Cells
MDPI
Müller et al. (2023) Plakophilin 3 facilitates G1/S phase transition and enhances proliferation by capturing RB protein in the cytoplasm and promoting EGFR signaling
Cell Reports
Luo et al. (2023) The long non-coding RNA LINC00958 is induced in psoriasis epidermis and modulates epidermal proliferation
Journal of Investigative Dermatology
Staebler et al. (2023) MIA/CD-RAP Regulates MMP13 and Is a Potential New Disease-Modifying Target for Osteoarthritis Therapy
MDPI
Hertel et al. (2022) USP32-regulated LAMTOR1 ubiquitination impacts mTORC1 activation and autophagy induction
Cell Reports
Yayon et al. (2022) High-throughput morphometric and transcriptomic profiling uncovers composition of naïve and sensory-deprived cortical cholinergic VIP/CHAT neurons
The EMBO Journal
Kim et al. (2022) Screening of the siGPCR library in combination with cisplatin against lung cancers
Scientific Reports
Mitani et al. (2022) SNAP23-Mediated Perturbation of Cholesterol-Enriched Membrane Microdomain Promotes Extracellular Vesicle Production in Src-Activated Cancer Cells
Biological and Pharmaceutical Bulletin
Blümel et al. (2022) Primary cilia contribute to the aggressiveness of atypical teratoid/rhabdoid tumors
Cell Death & Disease
Rovira et al. (2022) The lysosomal proteome of senescent cells contributes to the senescence secretome
Aging Cell
Koch et al. (2022) Targeting the Retinoblastoma/E2F repressive complex by CDK4/6 inhibitors amplifies oncolytic potency of an oncolytic adenovirus
Nature Communications
Schaefer et al. (2022) Global and precise identification of functionalmiRNA targets in mESCs by integrative analysis
EMBO Reports
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
Bartl et al. (2022) The HHIP-AS1 lncRNA promotes tumorigenicity through stabilization of dynein complex 1 in human SHH-driven tumors
Nature Communications
Banas et al. (2022) The Interplay of NEAT1 and miR-339-5p Influences on Mesangial Gene Expression and Function in Various Diabetic-Associated Injury Models
non-coding RNA
Mestre-Farràs et al. (2022) Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis
Nucleic Acids Research
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
Weihua Qin et. Al (2022) Probing protein ubiquitination in live cells
bioRxiv - preprint
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 N
ature 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.
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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.
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Ilina, E. I. et al. Effects of soluble CPE on glioma cell migration are associated with mTOR activation and enhanced glucose flux.
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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
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STEM CELLS Translational Medicine. (2017) doi:10.1002/sctm.17-0059
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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.
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Goyal, A. et al. Challenges of CRISPR/Cas9 applications for long non-coding RNA genes
Nucleic Acids Res. (2016)
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Nucleic Acids Res. (2015)
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