Total: 166 publication(s)


Achim K, Eling N, Vergara HM, Bertucci PY, Musser J, Vopalensky P, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. (2018)

Whole-body single-cell sequencing reveals transcriptional domains in the annelid larval body

Mol Biol Evol.


Goyal A, Fiškin E, Gutschner T, Polycarpou-Schwarz M, Groß M, Neugebauer J, Gandhi M, Caudron-Herger M, Benes V, Diederichs S. (2017)

A cautionary tale of sense-antisense gene pairs: independent regulation despite inverse correlation of expression.

Nucleic Acids Res. 45(21):12496-12508. doi: 10.1093/nar/gkx952
Europe PMC | doi

Schumacher E, Götze S, Kordes C, Benes V, Häussinger D. (2017)

Combined methylome and transcriptome analysis during rat hepatic stellate cell activation.

Stem Cells Dev. 26(24):1759-1770. doi: 10.1089/scd.2017.0128
Europe PMC | doi

Kole K, Komuro Y, Provaznik J, Pistolic J, Benes V, Tiesinga P, Celikel T. (2017)

Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation.

Gigascience 6(10):1-6. doi: 10.1093/gigascience/gix081
Europe PMC | doi

Morgan M, Much C, DiGiacomo M, Azzi C, Ivanova I, Vitsios DM, Pistolic J, Collier P, Moreira PN, Benes V, Enright AJ, O'Carroll D. (2017)

mRNA 3' uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome.

Nature 548(7667):347-351. doi: 10.1038/nature23318
Europe PMC | doi

Richa K, Balestra C, Piredda R, Benes V, Borra M, Passarelli A, Margiotta F, Saggiomo M, Biffali E, Sanges R, Scanlan DJ, Casotti R. (2017)

Distribution, community composition and potential metabolic activity of bacterioplankton in an urbanized Mediterranean Sea coastal zone.

Appl. Environ. Microbiol. 83(17) doi: 10.1128/AEM.00494-17
Europe PMC | doi

Pajer P, Dresler J, Kabíckova H, Písa L, Aganov P, Fucik K, Elleder D, Hron T, Kuzelka V, Velemínsky P, Klimentova J, Fucikova A, Pejchal J, Hrabakova R, Benes V, Rausch T, Dundr P, Pilin A, Cabala R, Hubalek M, Stríbrny J, Antwerpen MH, Meyer H. (2017)

Characterization of Two Historic Smallpox Specimens from a Czech Museum.

Viruses 9(8) doi: 10.3390/v9080200
Europe PMC | doi

Rodrigues PM, Ribeiro AR, Perrod C, Landry JJM, Araújo L, Pereira-Castro I, Benes V, Moreira A, Xavier-Ferreira H, Meireles C, Alves NL. (2017)

Thymic epithelial cells require p53 to support their long-term function in thymopoiesis in mice.

Blood 130(4):478-488. doi: 10.1182/blood-2016-12-758961
Europe PMC | doi

Chaipan C, Pryszlak A, Dean H, Poignard P, Benes V, Griffiths AD, Merten CA. (2017)

Single-Virus Droplet Microfluidics for High-Throughput Screening of Neutralizing Epitopes on HIV Particles.

Cell Chem Biol 24(6):751-757. doi: 10.1016/j.chembiol.2017.05.009
Europe PMC | doi

Pawlak M, Kikulska A, Wrzesinski T, Rausch T, Kwias Z, Wilczynski B, Benes V, Wesoly J, Wilanowski T. (2017)

Potential Protective Role of Grainyhead-like Genes in the Development of Clear Cell Renal Cell Carcinoma.

Mol Carcinog doi: 10.1002/mc.22682
Europe PMC | doi

Cabezas-Wallscheid N, Buettner F, Sommerkamp P, Klimmeck D, Ladel L, Thalheimer FB, Pastor-Flores D, Roma LP, Renders S, Zeisberger P, Przybylla A, Schönberger K, Scognamiglio R, Altamura S, Florian CM, Fawaz M, Vonficht D, Tesio M, Collier P, Pavlinic D, Geiger H, Schroeder T, Benes V, Dick TP, Rieger MA, Stegle O, Trumpp A. (2017)

Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.

Cell 169(5):807-823. doi: 10.1016/j.cell.2017.04.018
Europe PMC | doi

Jaruskova M, Curik N, Hercog R, Polivkova V, Motlova E, Benes V, Klamova H, Pecherkova P, Belohlavkova P, Vrbacky F, Machova Polakova K. (2017)

Genotypes of SLC22A4 and SLC22A5 regulatory loci are predictive of the response of chronic myeloid leukemia patients to imatinib treatment.

J Exp Clin Cancer Res 36(1):1-17. doi: 10.1186/s13046-017-0523-3
Europe PMC | doi

Gutierrez-Vazquez C, Enright AJ, Rodríguez-Galán A, Perez-García A, Collier P, Jones MR, Benes V, Mizgerd JP, Mittelbrunn M, Ramiro AR, Sanchez-Madrid F. (2017)

3'uridylation controls mature microRNA turnover during CD4 T cell activation.

RNA doi: 10.1261/rna.060095.116
Europe PMC | doi

Lorenzi L, Döring C, Rausch T, Benes V, Lonardi S, Bugatti M, Campo E, Cabeçadas J, Simonitsch-Klupp I, Borges A, Mehta J, Agostinelli C, Pileri SA, Facchetti F, Hansmann ML, Hartmann S. (2017)

Identification of novel follicular dendritic cell sarcoma markers, FDCSP and SRGN, by whole transcriptome sequencing.

Oncotarget 8(10):16463-16472. doi: 10.18632/oncotarget.14864
Europe PMC | doi

Richter-Pechańska P, Kunz JB, Hof J, Zimmermann M, Rausch T, Bandapalli OR, Orlova E, Scapinello G, Sagi JC, Stanulla M, Schrappe M, Cario G, Kirschner-Schwabe R, Eckert C, Benes V, Korbel JO, Muckenthaler MU, Kulozik AE. (2017)

Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia.

Blood Cancer J 7(2):e523. doi: 10.1038/bcj.2017.3
Europe PMC | doi

De Santi C, Vencken S, Blake J, Haase B, Benes V, Gemignani F, Landi S, Greene CM. (2017)

Identification of MiR-21-5p as a Functional Regulator of Mesothelin Expression Using MicroRNA Capture Affinity Coupled with Next Generation Sequencing.

PLoS ONE 12(1):e0170999. doi: 10.1371/journal.pone.0170999
Europe PMC | doi

Franzen J, Zirkel A, Blake J, Rath B, Benes V, Papantonis A, Wagner W. (2017)

Senescence-associated DNA methylation is stochastically acquired in subpopulations of mesenchymal stem cells.

Aging Cell 16(1):183-191. doi: 10.1111/acel.12544
Europe PMC | doi


Koehler C, Sauter PF, Wawryszyn M, Girona GE, Gupta K, Landry JJ, Fritz MH, Radic K, Hoffmann JE, Chen ZA, Zou J, Tan PS, Galik B, Junttila S, Stolt-Bergner P, Pruneri G, Gyenesei A, Schultz C, Biskup MB, Besir H, Benes V, Rappsilber J, Jechlinger M, Korbel JO, Berger I, Braese S, Lemke EA. (2016)

Genetic code expansion for multiprotein complex engineering.

Nat. Methods doi: 10.1038/nmeth.4032
Europe PMC | doi

Hollerer I, Curk T, Haase B, Benes V, Hauer C, Neu-Yilik G, Bhuvanagiri M, Hentze MW, Kulozik AE. (2016)

The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion.

RNA 22:1441-1453. doi: 10.1261/rna.055657.115
Europe PMC | doi

Arribas-Hernández L, Marchais A, Poulsen C, Haase B, Hauptmann J, Benes V, Meister G, Brodersen P. (2016)

The Slicer Activity of ARGONAUTE1 is Required Specifically for the Phasing, Not Production, of Trans-Acting Short Interfering RNAs in Arabidopsis.

Plant Cell doi: 10.1105/tpc.16.00121
Europe PMC | doi

Much C, Auchynnikava T, Pavlinic D, Buness A, Rappsilber J, Benes V, Allshire R, O'Carroll D. (2016)

Endogenous Mouse Dicer Is an Exclusively Cytoplasmic Protein.

PLoS Genet. 12(6):e1006095. doi: 10.1371/journal.pgen.1006095
Europe PMC | doi

Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P. (2016)

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

Science 352(6285):586-589. doi: 10.1126/science.aad8852
Europe PMC | doi

Naarmann-de Vries IS, Brendle A, Bähr-Ivacevic T, Benes V, Ostareck DH, Ostareck-Lederer A. (2016)

HnRNP K-mediated translational control links NMHC IIA to erythroid enucleation.

J. Cell. Sci. 129(6):1141-1154. doi: 10.1242/jcs.174995
Europe PMC | doi


Seckinger A, Meißner T, Moreaux J, Benes V, Hillengass J, Castoldi M, Zimmermann J, Ho AD, Jauch A, Goldschmidt H, Klein B, Hose D. (2015)

miRNAs in multiple myeloma - a survival relevant complex regulator of gene expression.

Oncotarget doi: 10.18632/oncotarget.5381
Europe PMC | doi

Lin Q, Chauvistré H, Costa IG, Gusmao EG, Mitzka S, Hänzelmann S, Baying B, Klisch T, Moriggl R, Hennuy B, Smeets H, Hoffmann K, Benes V, Seré K, Zenke M. (2015)

Epigenetic program and transcription factor circuitry of dendritic cell development.

Nucleic Acids Res 43(20):9680-9693. doi: 10.1093/nar/gkv1056
Europe PMC | doi

Petrella V, Aceto S, Musacchia F, Colonna V, Robinson M, Benes V, Cicotti G, Bongiorno G, Gradoni L, Volf P, Salvemini M. (2015)

De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum.

BMC Genomics 16 doi: 10.1186/s12864-015-2088-x
Europe PMC | doi

Poupardin R, Schöttner K, Korbelová J, Provazník J, Doležel D, Pavlinic D, Beneš V, Koštál V. (2015)

Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata.

BMC Genomics 16(1):720. doi: 10.1186/s12864-015-1907-4
Europe PMC | doi

Kunz JB, Rausch T, Bandapalli OR, Eilers J, Pechanska P, Schuessele S, Assenov Y, Stütz AM, Kirschner-Schwabe R, Hof J, Eckert C, von Stackelberg A, Schrappe M, Stanulla M, Koehler R, Avigad S, Elitzur S, Handgretinger R, Benes V, Weischenfeldt J, Korbel JO, Muckenthaler MU, Kulozik AE. (2015)

Pediatric T-lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation.

Haematologica 100 doi: 10.3324/haematol.2015.129692
Europe PMC | doi

Bleckmann M, Fritz MHY, Bhuju S, Jarek M, Schurig M, Geffers R, Benes V, Besir H, van den Heuvel J. (2015)

Genomic Analysis and Isolation of RNA Polymerase II Dependent Promoters from Spodoptera frugiperda

PLoS One 10(8):e0132898. doi: 10.1371/journal.pone.0132898
Europe PMC | doi

Lopez JP, Diallo A, Cruceanu C, Fiori LM, Laboissiere S, Guillet I, Fontaine J, Ragoussis J, Benes V, Turecki G, Ernst C. (2015)

Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing.

BMC Med Genomics 8:35. doi: 10.1186/s12920-015-0109-x
Europe PMC | doi

Frese KS, Meder B, Keller A, Just S, Haas J, Vogel B, Fischer S, Backes C, Matzas M, Köhler D, Benes V, Katus HA, Rottbauer W. (2015)

RNA splicing regulated by RBFOX1 is essential for cardiac function in zebrafish.

J. Cell. Sci. doi: 10.1242/jcs.166850
Europe PMC | doi

Benes V, Collier P, Kordes C, Stolte J, Rausch T, Muckentaler MU, Häussinger D, Castoldi M. (2015)

Identification of cytokine-induced modulation of microRNA expression and secretion as measured by a novel microRNA specific qPCR assay.

Sci Rep 5:11590. doi: 10.1038/srep11590
Europe PMC | doi

Ruijter JM, Lefever S, Anckaert J, Hellemans J, Pfaffl MW, Benes V, Bustin SA, Vandesompele J, Untergasser A, RDML consortium. (2015)

RDML-Ninja and RDMLdb for standardized exchange of qPCR data.

BMC Bioinformatics 16 doi: 10.1186/s12859-015-0637-6
Europe PMC | doi

Sidova M, Sindelka R, Castoldi M, Benes V, Kubista M. (2015)

Intracellular microRNA profiles form in the Xenopus laevis oocyte that may contribute to asymmetric cell division.

Sci Rep 5 doi: 10.1038/srep11157
Europe PMC | doi

Agarwal P, Collier P, Fritz MH, Benes V, Wiklund HJ, Westermark B, Singh U. (2015)

CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.

BMC Genomics 16(1):390. doi: 10.1186/s12864-015-1593-2
Europe PMC | doi

Costa M, Cruz E, Oliveira S, Benes V, Ivacevic T, Silva MJ, Vieira I, Dias F, Fonseca S, Gonçalves M, Lima M, Leitão C, Muckenthaler MU, Pinto J, Porto G. (2015)

Lymphocyte Gene Expression Signatures from Patients and Mouse Models of Hereditary Hemochromatosis Reveal a Function of HFE as a Negative Regulator of CD8+ T-Lymphocyte Activation and Differentiation In Vivo.

PLoS ONE 10(4) doi: 10.1371/journal.pone.0124246
Europe PMC | doi

Hänzelmann S, Beier F, Gusmao EG, Koch CM, Hummel S, Charapitsa I, Joussen S, Benes V, Brümmendorf TH, Reid G, Costa IG, Wagner W. (2015)

Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites

Clin Epigenetics 7(1):19. doi: 10.1186/s13148-015-0057-5
Europe PMC | doi

Pawlak M, Walkowska A, Mlącki M, Pistolic J, Wrzesiński T, Benes V, Jane SM, Wesoły J, Kompanowska-Jezierska E, Wilanowski T. (2015)

Consequences of the loss of the Grainyhead-like 1 gene for renal gene expression, regulation of blood pressure and heart rate in a mouse model.

Acta Biochim. Pol. 62(1):287-296. doi: 10.18388/abp.2015_1001
Europe PMC | doi

Thewes V, Simon R, Schroeter P, Schlotter M, Anzeneder T, Büttner R, Benes V, Sauter G, Burwinkel B, Nicholson RI, Sinn HP, Schneeweiss A, Deuschle U, Zapatka M, Heck S, Lichter P. (2015)

Reprogramming of the ERRα and ERα Target Gene Landscape Triggers Tamoxifen Resistance in Breast Cancer.

Cancer Res. 75:720. doi: 10.1158/0008-5472.CAN-14-0652
Europe PMC | doi

Karamitros D, Patmanidi AL, Kotantaki P, Potocnik AJ, Bähr-Ivacevic T, Benes V, Lygerou Z, Kioussis D, Taraviras S. (2015)

Geminin deletion increases the number of fetal hematopoietic stem cells by affecting the expression of key transcription factors.

Development 142(1):70-81. doi: 10.1242/dev.109454
Europe PMC | doi


Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. (2014)

Potential of fecal microbiota for early-stage detection of colorectal cancer.

Mol. Syst. Biol. 10(11):766. doi: 10.15252/msb.20145645
Europe PMC | doi

Gilsbach R, Preissl S, Grüning BA, Schnick T, Burger L, Benes V, Würch A, Bönisch U, Günther S, Backofen R, Fleischmann BK, Schübeler D, Hein L. (2014)

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease.

Nat Commun 5:Article No:5288. doi: 10.1038/ncomms6288
Europe PMC | doi

Tonigold M, Rossmann A, Meinold M, Bette M, Märken M, Henkenius K, Bretz AC, Giel G, Cai C, Rodepeter FR, Beneš V, Grénman R, Carey TE, Lage H, Stiewe T, Neubauer A, Werner JA, Brendel C, Mandic R. (2014)

A cisplatin-resistant head and neck cancer cell line with cytoplasmic p53(mut) exhibits ATP-binding cassette transporter upregulation and high glutathione levels.

J. Cancer Res. Clin. Oncol. 140(10):1689-1704. doi: 10.1007/s00432-014-1727-y
Europe PMC | doi

Hájková H, Fritz M, Haškovec C, Schwarz J, Šálek C, Marková J, Krejčík ZK, Dostálová Merkerová M, Kostečka AT, Vostrý M, Fuchs O, Michalová K, Cetkovský P, Beneš V. (2014)

CBFB - MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia.

J Hematol Oncol 7(1) doi: 10.1186/s13045-014-0066-4
Europe PMC | doi

Spornraft M, Kirchner B, Haase B, Benes V, Pfaffl MW, Riedmaier I. (2014)

Optimization of Extraction of Circulating RNAs from Plasma - Enabling Small RNA Sequencing

PLoS ONE 9(9):e107259. doi: 10.1371/journal.pone.0107259
Europe PMC | doi

Loehrer M, Vogel A, Huettel B, Reinhardt R, Benes V, Duplessis S, Usadel B, Schaffrath U. (2014)

On the current status of Phakopsora pachyrhizi genome sequencing

Front Plant Sci 5:377. doi: 10.3389/fpls.2014.00377
Europe PMC | doi

Gonzalez OG, Assfalg R, Koch S, Schelling A, Meena JK, Kraus J, Lechel A, Katz SF, Benes V, Scharffetter-Kochanek K, Kestler HA, Günes C, Iben S. (2014)

Telomerase stimulates ribosomal DNA transcription under hyperproliferative conditions

Nat Commun 5:Article No:4599. doi: 10.1038/ncomms5599
Europe PMC | doi

Vargel O, Zhang Y, Collier P, Baying B, Benes V, Lancrin C. (2014)

TGFβ pathway activation blocks the endothelial to hematopoietic transition

Paper presented at the ISEH 43rd Annual Scientific Meeting, Montréal, Canada, 21-24 August 2014.EXP HEMATOL 42(8):S64. doi: 10.1016/j.exphem.2014.07.243
Europe PMC | doi

Kminkova J, Mraz M, Zaprazna K, Navrkalova V, Tichy B, Plevova K, Malcikova J, Cerna K, Rausch T, Benes V, Brychtova Y, Doubek M, Mayer J, Pospisilova S. (2014)

Identification of novel sequence variations in microRNAs in chronic lymphocytic leukemia.

Carcinogenesis 35(5):992-1002. doi: 10.1093/carcin/bgt396
Europe PMC | doi

Blake J, Riddell A, Theiss S, Gonzalez AP, Haase B, Jauch A, Janssen JW, Ibberson D, Pavlinic D, Moog U, Benes V, Runz H. (2014)

Sequencing of a patient with balanced chromosome abnormalities and neurodevelopmental disease identifies disruption of multiple high risk loci by structural variation

PLoS ONE 9(3):e90894. doi: 10.1371/journal.pone.0090894
Europe PMC | doi

Gupta I, Clauder-Münster S, Klaus B, Järvelin AI, Aiyar RS, Benes V, Wilkening S, Huber W, Pelechano V, Steinmetz LM. (2014)

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions

Mol. Syst. Biol. 10(2):719. doi: 10.1002/msb.135068
Europe PMC | doi

Paakinaho V, Kaikkonen S, Makkonen H, Benes V, Palvimo JJ. (2014)

SUMOylation regulates the chromatin occupancy and anti-proliferative gene programs of glucocorticoid receptor

Nucleic Acids Res. 42(3):1575-1592. doi: 10.1093/nar/gkt1033
Europe PMC | doi

Pougach K, Voet A, Kondrashov FA, Voordeckers K, Christiaens JF, Baying B, Benes V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen KJ. (2014)

Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network

Nat Commun 5:4868. doi: 10.1038/ncomms5868
Europe PMC | doi


Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG. (2013)

Accounting for technical noise in single-cell RNA-seq experiments

Nat. Methods 10(11):1093-1095. doi: 10.1038/nmeth.2645
Europe PMC | doi

Bustin SA, Benes V, Garson J, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley G, Wittwer CT, Schjerling P, Day PJ, Abreu M, Aguado B, Beaulieu JF, Beckers A, Bogaert S, Browne JA, Carrasco-Ramiro F, Ceelen L, Ciborowski K, Cornillie P, Coulon S, Cuypers A, De Brouwer S, De Ceuninck L, De Craene J, De Naeyer H, De Spiegelaere W, Deckers K, Dheedene A, Durinck K, Ferreira-Teixeira M, Fieuw A, Gallup JM, Gonzalo-Flores S, Goossens K, Heindryckx F, Herring E, Hoenicka H, Icardi L, Jaggi R, Javad F, Karampelias M, Kibenge F, Kibenge M, Kumps C, Lambertz I, Lammens T, Markey A, Messiaen P, Mets E, Morais S, Mudarra-Rubio A, Nakiwala J, Nelis H, Olsvik PA, Pérez-Novo C, Plusquin M, Remans T, Rihani A, Rodrigues-Santos P, Rondou P, Sanders R, Schmidt-Bleek K, Skovgaard K, Smeets K, Tabera L, Toegel S, Van Acker T, Van den Broeck W, Van der Meulen J, Van Gele M, Van Peer G, Van Poucke M, Van Roy N, Vergult S, Wauman J, Tshuikina-Wiklander M, Willems E, Zaccara S, Zeka F, Vandesompele J. (2013)

The need for transparency and good practices in the qPCR literature

Nat. Methods 10(11):1063-1067. doi: 10.1038/nmeth.2697
Europe PMC | doi

Frühmesser A, Blake J, Haberlandt E, Baying B, Raeder B, Runz H, Spreiz A, Fauth C, Benes V, Utermann G, Zschocke J, Kotzot D. (2013)

Disruption of EXOC6B in a patient with developmental delay, epilepsy, and a de novo balanced t(2;8) translocation

Eur. J. Hum. Genet. 21(10):1177-1180. doi: 10.1038/ejhg.2013.18
Europe PMC | doi

Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow RC, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills RE, Park PJ, Lee C, Korbel JO. (2013)

Primate genome architecture influences structural variation mechanisms and functional consequences

Proc. Natl. Acad. Sci. U.S.A. 110(39):15764-15769. doi: 10.1073/pnas.1305904110
Europe PMC | doi

Wilkening S, Pelechano V, Jarvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM. (2013)

An efficient method for genome-wide polyadenylation site mapping and RNA quantification (vol 41, pg e65, 2013)

Nucleic Acids Res 41(12):6370. doi: 10.1093/nar/gkt364

Huggett JF, Foy CA, Benes V, Emslie K, Garson JA, Haynes R, Hellemans J, Kubista M, Mueller RD, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT, Bustin SA. (2013)

The digital MIQE guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments

Clin. Chem. 59(6):892-902. doi: 10.1373/clinchem.2013.206375
Europe PMC | doi

Di Giacomo M, Comazzetto S, Saini H, De Fazio S, Carrieri C, Morgan M, Vasiliauskaite L, Benes V, Enright AJ, O'Carroll D. (2013)

Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis

Mol. Cell 50(4):601-608. doi: 10.1016/j.molcel.2013.04.026
Europe PMC | doi

Wilkening S, Pelechano V, Järvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM. (2013)

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

Nucleic Acids Res. 41(12):6370. doi: 10.1093/nar/gks1249
Europe PMC | doi

Weischenfeldt J, Simon R, Feuerbach L, Schlangen K, Weichenhan D, Minner S, Wuttig D, Warnatz HJ, Stehr H, Rausch T, Jäger N, Gu L, Bogatyrova O, Stütz AM, Claus R, Eils J, Eils R, Gerhäuser C, Huang PH, Hutter B, Kabbe R, Lawerenz C, Radomski S, Bartholomae CC, Fälth M, Gade S, Schmidt M, Amschler N, Haß T, Galal R, Gjoni J, Kuner R, Baer C, Masser S, von Kalle C, Zichner T, Benes V, Raeder B, Mader M, Amstislavskiy V, Avci M, Lehrach H, Parkhomchuk D, Sultan M, Burkhardt L, Graefen M, Huland H, Kluth M, Krohn A, Sirma H, Stumm L, Steurer S, Grupp K, Sültmann H, Sauter G, Plass C, Brors B, Yaspo ML, Korbel JO, Schlomm T. (2013)

Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer

Cancer Cell 23(2):159-170. doi: 10.1016/j.ccr.2013.01.002
Europe PMC | doi

Bettencourt P, Marion S, Pires D, Santos LF, Lastrucci C, Carmo N, Blake J, Benes V, Griffiths G, Neyrolles O, Lugo-Villarino G, Anes E. (2013)

Actin-binding protein regulation by microRNAs as a novel microbial strategy to modulate phagocytosis by host cells: the case of N-Wasp and miR-142-3p

Front Cell Infect Microbiol 3:19. doi: 10.3389/fcimb.2013.00019
Europe PMC | doi


Schubert T, Pusch MC, Diermeier S, Benes V, Kremmer E, Imhof A, Längst G. (2012)

Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin

Mol. Cell 48(3):434-444. doi: 10.1016/j.molcel.2012.08.021
Europe PMC | doi

Paris O, Ferraro L, Grober OM, Ravo M, De Filippo MR, Giurato G, Nassa G, Tarallo R, Cantarella C, Rizzo F, Di Benedetto A, Mottolese M, Benes V, Ambrosino C, Nola E, Weisz A. (2012)

Direct regulation of microRNA biogenesis and expression by estrogen receptor beta in hormone-responsive breast cancer

Oncogene 31(38):4196-4206. doi: 10.1038/onc.2011.583
Europe PMC | doi

Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. (2012)

DELLY: structural variant discovery by integrated paired-end and split-read analysis

Paper presented at the 11th European Conference on Computational Biology (ECCB) / Conference of the Intelligent Systems in Molecular Biology (ISMB), Basel, SWITZERLAND, SEP 09-12, 2012.Bioinformatics 28(18):i333-i339. doi: 10.1093/bioinformatics/bts378
Europe PMC | doi

Xiol J, Cora E, Koglgruber R, Chuma S, Subramanian S, Hosokawa M, Reuter M, Yang Z, Berninger P, Palencia A, Benes V, Penninger J, Sachidanandam R, Pillai RS. (2012)

A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing

Mol. Cell 47(6):970-979. doi: 10.1016/j.molcel.2012.07.019
Europe PMC | doi

Jones DT, Jäger N, Kool M, Zichner T, Hutter B, Sultan M, Cho YJ, Pugh TJ, Hovestadt V, Stütz AM, Rausch T, Warnatz HJ, Ryzhova M, Bender S, Sturm D, Pleier S, Cin H, Pfaff E, Sieber L, Wittmann A, Remke M, Witt H, Hutter S, Tzaridis T, Weischenfeldt J, Raeder B, Avci M, Amstislavskiy V, Zapatka M, Weber UD, Wang Q, Lasitschka B, Bartholomae CC, Schmidt M, von Kalle C, Ast V, Lawerenz C, Eils J, Kabbe R, Benes V, van Sluis P, Koster J, Volckmann R, Shih D, Betts MJ, Russell RB, Coco S, Tonini GP, Schüller U, Hans V, Graf N, Kim YJ, Monoranu C, Roggendorf W, Unterberg A, Herold-Mende C, Milde T, Kulozik AE, von Deimling A, Witt O, Maass E, Rössler J, Ebinger M, Schuhmann MU, Frühwald MC, Hasselblatt M, Jabado N, Rutkowski S, von Bueren AO, Williamson D, Clifford SC, McCabe MG, Collins VP, Wolf S, Wiemann S, Lehrach H, Brors B, Scheurlen W, Felsberg J, Reifenberger G, Northcott PA, Taylor MD, Meyerson M, Pomeroy SL, Yaspo ML, Korbel JO, Korshunov A, Eils R, Pfister SM, Lichter P. (2012)

Dissecting the genomic complexity underlying medulloblastoma

Nature 488(7409):100-105. doi: 10.1038/nature11284
Europe PMC | doi

Riedmaier I, Benes V, Blake J, Bretschneider N, Zinser C, Becker C, Meyer HH, Pfaffl MW. (2012)

RNA-sequencing as useful screening tool in the combat against the misuse of anabolic agents

Anal. Chem. 84(15):6863-6868. doi: 10.1021/ac301433d
Europe PMC | doi

Preussner M, Schreiner S, Hung LH, Porstner M, Jäck HM, Benes V, Rätsch G, Bindereif A. (2012)

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing

Nucleic Acids Res. 40(12):5666-5678. doi: 10.1093/nar/gks221
Europe PMC | doi

Simpson JC, Joggerst B, Laketa V, Verissimo F, Cetin C, Erfle H, Bexiga MG, Singan VR, Hériché JK, Neumann B, Mateos A, Blake J, Bechtel S, Benes V, Wiemann S, Ellenberg J, Pepperkok R. (2012)

Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway

Nat. Cell Biol. 14(7):764-774. doi: 10.1038/ncb2510
Europe PMC | doi

Baay-Guzman GJ, Huerta-Yepez S, Vega MI, Aguilar-Leon D, Campillos M, Blake J, Benes V, Hernandez-Pando R, Teran LM. (2012)

Role of CXCL13 in asthma: novel therapeutic target

Chest 141(4):886-894. doi: 10.1378/chest.11-0633
Europe PMC | doi

Benesova K, Vujić Spasić M, Schaefer SM, Stolte J, Baehr-Ivacevic T, Waldow K, Zhou Z, Klingmueller U, Benes V, Mall MA, Muckenthaler MU. (2012)

Hfe deficiency impairs pulmonary neutrophil recruitment in response to inflammation

PLoS ONE 7(6):e39363. doi: 10.1371/journal.pone.0039363
Europe PMC | doi

Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee AS. (2012)

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

Nat Commun 3:886. doi: 10.1038/ncomms1878
Europe PMC | doi

Rausch T, Jones DT, Zapatka M, Stütz AM, Zichner T, Weischenfeldt J, Jäger N, Remke M, Shih D, Northcott PA, Pfaff E, Tica J, Wang Q, Massimi L, Witt H, Bender S, Pleier S, Cin H, Hawkins C, Beck C, von Deimling A, Hans V, Brors B, Eils R, Scheurlen W, Blake J, Benes V, Kulozik AE, Witt O, Martin D, Zhang C, Porat R, Merino DM, Wasserman J, Jabado N, Fontebasso A, Bullinger L, Rücker FG, Döhner K, Döhner H, Koster J, Molenaar JJ, Versteeg R, Kool M, Tabori U, Malkin D, Korshunov A, Taylor MD, Lichter P, Pfister SM, Korbel JO. (2012)

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

Cell 148(1-2):59-71. doi: 10.1016/j.cell.2011.12.013
Europe PMC | doi


Suffert G, Malterer G, Hausser J, Viiliäinen J, Fender A, Contrant M, Ivacevic T, Benes V, Gros F, Voinnet O, Zavolan M, Ojala PM, Haas JG, Pfeffer S. (2011)

Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis

PLoS Pathog. 7(12):e1002405. doi: 10.1371/journal.ppat.1002405
Europe PMC | doi

Galmiche L, Serre V, Beinat M, Assouline Z, Lebre AS, Chretien D, Nietschke P, Benes V, Boddaert N, Sidi D, Brunelle F, Rio M, Munnich A, Rötig A. (2011)

Exome sequencing identifies MRPL3 mutation in mitochondrial cardiomyopathy

Hum. Mutat. 32(11):1225-1231. doi: 10.1002/humu.21562
Europe PMC | doi

Heikkinen S, Väisänen S, Pehkonen P, Seuter S, Benes V, Carlberg C. (2011)

Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy

Nucleic Acids Res. 39(21):9181-9193. doi: 10.1093/nar/gkr654
Europe PMC | doi

Sanchez M, Galy B, Schwanhaeusser B, Blake J, Bähr-Ivacevic T, Benes V, Selbach M, Muckenthaler MU, Hentze MW. (2011)

Iron regulatory protein-1 and -2: transcriptome-wide definition of binding mRNAs and shaping of the cellular proteome by iron regulatory proteins

Blood 118(22):e168-79. doi: 10.1182/blood-2011-04-343541
Europe PMC | doi

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. (2011)

Primer sequence disclosure: a clarification of the MIQE guidelines

Clin. Chem. 57(6):919-921. doi: 10.1373/clinchem.2011.162958
Europe PMC | doi

Rösel TD, Hung LH, Medenbach J, Donde K, Starke S, Benes V, Rätsch G, Bindereif A. (2011)

RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation

EMBO J. 30(10):1965-1976. doi: 10.1038/emboj.2011.106
Europe PMC | doi

Castoldi M, Vujic Spasic M, Altamura S, Elmén J, Lindow M, Kiss J, Stolte J, Sparla R, D'Alessandro LA, Klingmüller U, Fleming RE, Longerich T, Gröne HJ, Benes V, Kauppinen S, Hentze MW, Muckenthaler MU. (2011)

The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice

J. Clin. Invest. 121(4):1386-1396. doi: 10.1172/jci44883
Europe PMC | doi

Kahramanoglou C, Seshasayee AS, Prieto AI, Ibberson D, Schmidt S, Zimmermann J, Benes V, Fraser GM, Luscombe NM. (2011)

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli

Nucleic Acids Res. 39(6):2073-2091. doi: 10.1093/nar/gkq934
Europe PMC | doi

Takács L, Tóth E, Losonczy G, Szanto A, Bähr-Ivacevic T, Benes V, Berta A, Vereb G. (2011)

Differentially expressed genes associated with human limbal epithelial phenotypes: new molecules that potentially facilitate selection of stem cell-enriched populations

Invest. Ophthalmol. Vis. Sci. 52(3):1252-1260. doi: 10.1167/iovs.10-5242
Europe PMC | doi

Grober OM, Mutarelli M, Giurato G, Ravo M, Cicatiello L, De Filippo MR, Ferraro L, Nassa G, Papa MF, Paris O, Tarallo R, Luo S, Schroth GP, Benes V, Weisz A. (2011)

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

BMC Genomics 12:36. doi: 10.1186/1471-2164-12-36
Europe PMC | doi


Corbo JC, Lawrence KA, Karlstetter M, Myers CA, Abdelaziz M, Dirkes W, Weigelt K, Seifert M, Benes V, Fritsche LG, Weber BH, Langmann T. (2010)

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

Genome Res. 20(11):1512-1525. doi: 10.1101/gr.109405.110
Europe PMC | doi

Benes V, Castoldi M. (2010)

Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available

Methods 50(4):244-249. doi: 10.1016/j.ymeth.2010.01.026
Europe PMC | doi

Gavriouchkina D, Fischer S, Ivacevic T, Stolte J, Benes V, Dekens MP. (2010)

Thyrotroph embryonic factor regulates light-induced transcription of repair genes in zebrafish embryonic cells

PLoS ONE 5(9):e12542. doi: 10.1371/journal.pone.0012542
Europe PMC | doi


Witt N, Rodger G, Vandesompele J, Benes V, Zumla A, Rook GA, Huggett JF. (2009)

An assessment of air as a source of DNA contamination encountered when performing PCR

J Biomol Tech 20(5):236-240.
Europe PMC

Maillot G, Lacroix-Triki M, Pierredon S, Gratadou L, Schmidt S, Bénès V, Roché H, Dalenc F, Auboeuf D, Millevoi S, Vagner S. (2009)

Widespread estrogen-dependent repression of micrornas involved in breast tumor cell growth

Cancer Res. 69(21):8332-8340. doi: 10.1158/0008-5472.can-09-2206
Europe PMC | doi

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. (2009)

The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments

Clin. Chem. 55(4):611-622. doi: 10.1373/clinchem.2008.112797
Europe PMC | doi

Hose D, Rème T, Meissner T, Moreaux J, Seckinger A, Lewis J, Benes V, Benner A, Hundemer M, Hielscher T, Shaughnessy JD Jr, Barlogie B, Neben K, Krämer A, Hillengass J, Bertsch U, Jauch A, De Vos J, Rossi JF, Möhler T, Blake J, Zimmermann J, Klein B, Goldschmidt H. (2009)

Inhibition of aurora kinases for tailored risk-adapted treatment of multiple myeloma

Blood 113(18):4331-4340. doi: 10.1182/blood-2008-09-178350
Europe PMC | doi

Garson JA, Huggett JF, Bustin SA, Pfaffl MW, Benes V, Vandesompele J, Shipley GL. (2009)

Unreliable real-time PCR analysis of human endogenous retrovirus-W (HERV-W) RNA expression and DNA copy number in multiple sclerosis

AIDS Res. Hum. Retroviruses 25(3):377-8; author reply 379-81. doi: 10.1089/aid.2008.0270
Europe PMC | doi

Weinmann L, Höck J, Ivacevic T, Ohrt T, Mütze J, Schwille P, Kremmer E, Benes V, Urlaub H, Meister G. (2009)

Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs

Cell 136(3):496-507. doi: 10.1016/j.cell.2008.12.023
Europe PMC | doi

Benes V, Stolte J, Ibberson D, Castoldi M, Muckenthaler M. (2009)

Analysis of microribonucleic acid expression by quantitative real-time polymerase chain reaction

Cambridge University Press.doi: 10.1017/cbo9780511818974.008
Europe PMC | doi

Ibberson D, Benes V, Muckenthaler MU, Castoldi M. (2009)

RNA degradation compromises the reliability of microRNA expression profiling

BMC Biotechnol. 9:102. doi: 10.1186/1472-6750-9-102
Europe PMC | doi

Lowery AJ, Miller N, Devaney A, McNeill RE, Davoren PA, Lemetre C, Benes V, Schmidt S, Blake J, Ball G, Kerin MJ. (2009)

MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer

Breast Cancer Res. 11(3):R27. doi: 10.1186/bcr2257
Europe PMC | doi

Wagner W, Bork S, Horn P, Krunic D, Walenda T, Diehlmann A, Benes V, Blake J, Huber FX, Eckstein V, Boukamp P, Ho AD. (2009)

Aging and replicative senescence have related effects on human stem and progenitor cells

PLoS ONE 4(6):e5846. doi: 10.1371/journal.pone.0005846
Europe PMC | doi


Kangaspeska S, Stride B, Métivier R, Polycarpou-Schwarz M, Ibberson D, Carmouche RP, Benes V, Gannon F, Reid G. (2008)

Transient cyclical methylation of promoter DNA

Nature 452(7183):112-115. doi: 10.1038/nature06640
Europe PMC | doi

Métivier R, Gallais R, Tiffoche C, Le Péron C, Jurkowska RZ, Carmouche RP, Ibberson D, Barath P, Demay F, Reid G, Benes V, Jeltsch A, Gannon F, Salbert G. (2008)

Cyclical DNA methylation of a transcriptionally active promoter

Nature 452(7183):45-50. doi: 10.1038/nature06544
Europe PMC | doi