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Genomics Core FacilityPublications

Total: 122 publication(s)

2014

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 5:4599. doi:10.1038/ncomms5599
Europe PMC | doi

Vargel O, Zhang Y, Collier P, Baying B, Benes V, Lancrin C. (2014)
TGF beta PATHWAY ACTIVATION BLOCKS THE ENDOTHELIAL TO HEMATOPOIETIC TRANSITION
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

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

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

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

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


2013

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
doi

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(5):e65. 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


2012

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

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

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
Bioinformatics 28(18):i333-i339. doi:10.1093/bioinformatics/bts378
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

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

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

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

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

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

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

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


2011

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

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

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

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

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

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

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


2010

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


2009

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

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

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

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

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

Benes V, Stolte J, Ibberson D, Castoldi M, Muckenthaler M. (2009)
Analysis of microribonucleic acid expression by quantitative real-time polymerase chain reaction
doi:10.1017/cbo9780511818974.008
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

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


2008

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

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

Hung LH, Heiner M, Hui J, Schreiner S, Benes V, Bindereif A. (2008)
Diverse roles of hnRNP L in mammalian mRNA processing: a combined microarray and RNAi analysis
RNA 14(2):284-296. doi:10.1261/rna.725208
Europe PMC | doi

Denger S, Bähr-Ivacevic T, Brand H, Reid G, Blake J, Seifert M, Lin CY, May K, Benes V, Liu ET, Gannon F. (2008)
Transcriptome profiling of estrogen-regulated genes in human primary osteoblasts reveals an osteoblast-specific regulation of the insulin-like growth factor binding protein 4 gene
Mol. Endocrinol. 22(2):361-379. doi:10.1210/me.2007-0292
Europe PMC | doi

Castoldi M, Schmidt S, Benes V, Hentze MW, Muckenthaler MU. (2008)
miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes
Nat Protoc 3(2):321-329. doi:10.1038/nprot.2008.4
Europe PMC | doi

Wagner W, Horn P, Castoldi M, Diehlmann A, Bork S, Saffrich R, Benes V, Blake J, Pfister S, Eckstein V, Ho AD. (2008)
Replicative senescence of mesenchymal stem cells: a continuous and organized process
PLoS ONE 3(5):e2213. doi:10.1371/journal.pone.0002213
Europe PMC | doi


2007

Castoldi M, Benes V, Hentze MW, Muckenthaler MU. (2007)
miChip: a microarray platform for expression profiling of microRNAs based on locked nucleic acid (LNA) oligonucleotide capture probes
Methods 43(2):146-152. doi:10.1016/j.ymeth.2007.04.009
Europe PMC | doi

Koutsos AC, Blass C, Meister S, Schmidt S, MacCallum RM, Soares MB, Collins FH, Benes V, Zdobnov E, Kafatos FC, Christophides GK. (2007)
Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster
Proc. Natl. Acad. Sci. U.S.A. 104(27):11304-11309. doi:10.1073/pnas.0703988104
Europe PMC | doi

Kozmik Z, Holland ND, Kreslova J, Oliveri D, Schubert M, Jonasova K, Holland LZ, Pestarino M, Benes V, Candiani S. (2007)
Pax-Six-Eya-Dach network during amphioxus development: conservation in vitro but context specificity in vivo
Dev. Biol. 306(1):143-159. doi:10.1016/j.ydbio.2007.03.009
Europe PMC | doi

Burkart C, Qiu F, Brendel S, Benes V, Hååg P, Labeit S, Leonard K, Bullard B. (2007)
Modular proteins from the Drosophila sallimus (sls) gene and their expression in muscles with different extensibility
J. Mol. Biol. 367(4):953-969. doi:10.1016/j.jmb.2007.01.059
Europe PMC | doi

Wagner W, Wein F, Roderburg C, Saffrich R, Faber A, Krause U, Schubert M, Benes V, Eckstein V, Maul H, Ho AD. (2007)
Adhesion of hematopoietic progenitor cells to human mesenchymal stem cells as a model for cell-cell interaction
Exp. Hematol. 35(2):314-325. doi:10.1016/j.exphem.2006.10.003
Europe PMC | doi

Wagner W, Wein F, Roderburg C, Benes V, Frankhauser M, Wuchter P, Eckstein V, Ho AD. (2007)
Molecular composition of cell-cell contact between hematopoietic stem cells and mesenchymal stem cells
Biol. Blood Marrow Transplant. 13(2):47-48.
Europe PMC


2006

Castoldi M, Schmidt S, Benes V, Noerholm M, Kulozik AE, Hentze MW, Muckenthaler MU. (2006)
A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA)
RNA 12(5):913-920. doi:10.1261/rna.2332406
Europe PMC | doi

Bullard B, Garcia T, Benes V, Leake MC, Linke WA, Oberhauser AF. (2006)
The molecular elasticity of the insect flight muscle proteins projectin and kettin
Proc. Natl. Acad. Sci. U.S.A. 103(12):4451-4456. doi:10.1073/pnas.0509016103
Europe PMC | doi


2005

Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, Jubin C, Balavoine G, Ferrier D, Benes V, de Jong P, Weissenbach J, Bork P, Arendt D. (2005)
Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii
Science 310(5752):1325-1326. doi:10.1126/science.1119089
Europe PMC | doi

Reid G, Métivier R, Lin CY, Denger S, Ibberson D, Ivacevic T, Brand H, Benes V, Liu ET, Gannon F. (2005)
Multiple mechanisms induce transcriptional silencing of a subset of genes, including oestrogen receptor alpha, in response to deacetylase inhibition by valproic acid and trichostatin A
Oncogene 24(31):4894-4907. doi:10.1038/sj.onc.1208662
Europe PMC | doi

Bustin SA, Benes V, Nolan T, Pfaffl MW. (2005)
Quantitative real-time RT-PCR--a perspective
J. Mol. Endocrinol. 34(3):597-601. doi:10.1677/jme.1.01755
Europe PMC | doi

Relógio A, Ben-Dov C, Baum M, Ruggiu M, Gemund C, Benes V, Darnell RB, Valcárcel J. (2005)
Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells
J. Biol. Chem. 280(6):4779-4784. doi:10.1074/jbc.m411976200
Europe PMC | doi


2004

Métivier R, Penot G, Carmouche RP, Hübner MR, Reid G, Denger S, Manu D, Brand H, Kos M, Benes V, Gannon F. (2004)
Transcriptional complexes engaged by apo-estrogen receptor-alpha isoforms have divergent outcomes
EMBO J. 23(18):3653-3666. doi:10.1038/sj.emboj.7600377
Europe PMC | doi

Schilling O, Rüggeberg S, Vogel A, Rittner N, Weichert S, Schmidt S, Doig S, Franz T, Benes V, Andrews SC, Baum M, Meyer-Klaucke W. (2004)
Characterization of an Escherichia coli elaC deletion mutant
Biochem. Biophys. Res. Commun. 320(4):1365-1373. doi:10.1016/j.bbrc.2004.05.227
Europe PMC | doi

Galy B, Ferring D, Benesova M, Benes V, Hentze MW. (2004)
Targeted mutagenesis of the murine IRP1 and IRP2 genes reveals context-dependent RNA processing differences in vivo
RNA 10(7):1019-1025. doi:10.1261/rna.7220704
Europe PMC | doi

Pacheco TR, Gomes AQ, Barbosa-Morais NL, Benes V, Ansorge W, Wollerton M, Smith CW, Valcárcel J, Carmo-Fonseca M. (2004)
Diversity of vertebrate splicing factor U2AF35: identification of alternatively spliced U2AF1 mRNAS
J. Biol. Chem. 279(26):27039-27049. doi:10.1074/jbc.m402136200
Europe PMC | doi

Opitz CA, Leake MC, Makarenko I, Benes V, Linke WA. (2004)
Developmentally regulated switching of titin size alters myofibrillar stiffness in the perinatal heart
Circ. Res. 94(7):967-975. doi:10.1161/01.res.0000124301.48193.e1
Europe PMC | doi

Lange SA, Benes V, Kern DP, Hörber JK, Bernard A. (2004)
Microcontact printing of DNA molecules
Anal. Chem. 76(6):1641-1647. doi:10.1021/ac035127w
Europe PMC | doi

Testa G, Vintersten K, Zhang Y, Benes V, Muyrers JP, Stewart AF. (2004)
BAC engineering for the generation of ES cell-targeting constructs and mouse transgenes
Methods Mol. Biol. 256:123-139. doi:10.1385/1-59259-753-x:123
Europe PMC | doi

Muyrers JP, Zhang Y, Benes V, Testa G, Rientjes JM, Stewart AF. (2004)
ET recombination: DNA engineering using homologous recombination in E. coli
Methods Mol. Biol. 256:107-121. doi:10.1385/1-59259-753-x:107
Europe PMC | doi


2003

Benes V, Muckenthaler M. (2003)
Standardization of protocols in cDNA microarray analysis
Trends Biochem. Sci. 28(5):244-249. doi:10.1016/s0968-0004(03)00068-9
Europe PMC | doi

Testa G, Zhang Y, Vintersten K, Benes V, Pijnappel WW, Chambers I, Smith AJ, Smith AG, Stewart AF. (2003)
Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles
Nat. Biotechnol. 21(4):443-447. doi:10.1038/nbt804
Europe PMC | doi

Candiani S, Kreslova J, Benes V, Oliveri D, Castagnola P, Pestarino M, Kozmik Z. (2003)
Cloning and developmental expression of amphioxus Dachschund
Gene Expr. Patterns 3(1):65-69. doi:10.1016/s1567-133x(02)00070-4
Europe PMC | doi


2002

Jasper H, Benes V, Atzberger A, Sauer S, Ansorge W, Bohmann D. (2002)
A genomic switch at the transition from cell proliferation to terminal differentiation in the Drosophila eye
Dev. Cell 3(4):511-521. doi:10.1016/s1534-5807(02)00297-6
Europe PMC | doi

Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL. (2002)
The genome sequence of the malaria mosquito Anopheles gambiae
Science 298(5591):129-149. doi:10.1126/science.1076181
Europe PMC | doi

Krelová J, Holland LZ, Schubert M, Burgtorf C, Benes V, Kozmik Z. (2002)
Functional equivalency of amphioxus and vertebrate Pax258 transcription factors suggests that the activation of mid-hindbrain specific genes in vertebrates occurs via the recruitment of Pax regulatory elements
Gene 282(1-2):143-150. doi:10.1016/s0378-1119(01)00840-x
Europe PMC | doi


2001

Jasper H, Benes V, Schwager C, Sauer S, Clauder-Münster S, Ansorge W, Bohmann D. (2001)
The genomic response of the Drosophila embryo to JNK signaling
Dev. Cell 1(4):579-586. doi:10.1016/s1534-5807(01)00045-4
Europe PMC | doi


2000

Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blöcker H, Perez-Alonso M, Obermaier B, Delseny M, Boutry M, Grivell LA, Mache R, Puigdomènech P, De Simone V, Choisne N, Artiguenave F, Robert C, Brottier P, Wincker P, Cattolico L, Weissenbach J, Saurin W, Quétier F, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Benes V, Wurmbach E, Drzonek H, Erfle H, Jordan N, Bangert S, Wiedelmann R, Kranz H, Voss H, Holland R, Brandt P, Nyakatura G, Vezzi A, D'Angelo M, Pallavicini A, Toppo S, Simionati B, Conrad A, Hornischer K, Kauer G, Löhnert TH, Nordsiek G, Reichelt J, Scharfe M, Schön O, Bargues M, Terol J, Climent J, Navarro P, Collado C, Perez-Perez A, Ottenwälder B, Duchemin D, Cooke R, Laudie M, Berger-Llauro C, Purnelle B, Masuy D, de Haan M, Maarse AC, Alcaraz JP, Cottet A, Casacuberta E, Monfort A, Argiriou A, flores M, Liguori R, Vitale D, Mannhaupt G, Haase D, Schoof H, Rudd S, Zaccaria P, Mewes HW, Mayer KF, Kaul S, Town CD, Koo HL, Tallon LJ, Jenkins J, Rooney T, Rizzo M, Walts A, Utterback T, Fujii CY, Shea TP, Creasy TH, Haas B, Maiti R, Wu D, Peterson J, Van Aken S, Pai G, Militscher J, Sellers P, Gill JE, Feldblyum TV, Preuss D, Lin X, Nierman WC, Salzberg SL, White O, Venter JC, Fraser CM, Kaneko T, Nakamura Y, Sato S, Kato T, Asamizu E, Sasamoto S, Kimura T, Idesawa K, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S, European Union Chromosome 3 Arabidopsis Sequencing Consortium, Institute for Genomic Research, Kazusa DNA Research Institute. (2000)
Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana
Nature 408(6814):820-822. doi:10.1038/35048706
Europe PMC | doi

Fukami M, Kirsch S, Schiller S, Richter A, Benes V, Franco B, Muroya K, Rao E, Merker S, Niesler B, Ballabio A, Ansorge W, Ogata T, Rappold GA. (2000)
A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation
Am. J. Hum. Genet. 67(3):563-573. doi:10.1086/303047
Europe PMC | doi

Muyrers JP, Zhang Y, Benes V, Testa G, Ansorge W, Stewart AF. (2000)
Point mutation of bacterial artificial chromosomes by ET recombination
EMBO Rep. 1(3):239-243. doi:10.1093/embo-reports/kvd049
Europe PMC | doi

Hill F, Gemünd C, Benes V, Ansorge W, Gibson TJ. (2000)
An estimate of large-scale sequencing accuracy
EMBO Rep. 1(1):29-31. doi:10.1093/embo-reports/kvd015
Europe PMC | doi

Dimopoulos G, Casavant TL, Chang S, Scheetz T, Roberts C, Donohue M, Schultz J, Benes V, Bork P, Ansorge W, Soares MB, Kafatos FC. (2000)
Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines
Proc. Natl. Acad. Sci. U.S.A. 97(12):6619-6624. doi:10.1073/pnas.97.12.6619
Europe PMC | doi

De Michelis S, Sewell HS, Collares-Pereira M, Santos-Reis M, Schouls LM, Benes V, Holmes EC, Kurtenbach K. (2000)
Genetic diversity of Borrelia burgdorferi sensu lato in ticks from mainland Portugal
J. Clin. Microbiol. 38(6):2128-2133.
Europe PMC

Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansroge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Müller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Bountry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham SA, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang YJ, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Rose M. (2000)
Progress in Arabidopsis genome sequencing and functional genomics
J. Biotechnol. 78(3):281-292. doi:10.1016/s0168-1656(00)00195-4
Europe PMC | doi

Hill F, Benes V, Thomasova D, Stewart AF, Kafatos FC, Ansorge W. (2000)
BAC trimming: minimizing clone overlaps
Genomics 64(1):111-113. doi:10.1006/geno.1999.6106
Europe PMC | doi

Stopa M, Benes V, Ansorge W, Gressner AM, Dooley S. (2000)
Genomic locus and promoter region of rat Smad7, an important antagonist of TGFbeta signaling
Mamm. Genome 11(2):169-176. doi:10.1007/s003350010032
Europe PMC | doi

Kolmerer B, Clayton J, Benes V, Allen T, Ferguson C, Leonard K, Weber U, Knekt M, Ansorge W, Labeit S, Bullard B. (2000)
Sequence and expression of the kettin gene in Drosophila melanogaster and Caenorhabditis elegans
J. Mol. Biol. 296(2):435-448. doi:10.1006/jmbi.1999.3461
Europe PMC | doi


1999

Valcárcel R, Weber U, Jackson DB, Benes V, Ansorge W, Bohmann D, Mlodzik M. (1999)
Sec61beta, a subunit of the protein translocation channel, is required during Drosophila development
J. Cell. Sci. 112 ( Pt 23):4389-4396.
Europe PMC

Mayer K, Schüller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansorge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Müller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Boutry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham SA, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang YJ, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiaens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Ramsperger U, Hilbert H, Braun M, Holzer E, Brandt A, Peters S, van Staveren M, Dirske W, Mooijman P, Klein Lankhorst R, Rose M, Hauf J, Kötter P, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Van den Daele H, De Keyser A, Buysshaert C, Gielen J, Villarroel R, De Clercq R, Van Montagu M, Rogers J, Cronin A, Quail M, Bray-Allen S, Clark L, Doggett J, Hall S, Kay M, Lennard N, McLay K, Mayes R, Pettett A, Rajandream MA, Lyne M, Benes V, Rechmann S, Borkova D, Blöcker H, Scharfe M, Grimm M, Löhnert TH, Dose S, de Haan M, Maarse A, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Fartmann B, Granderath K, Dauner D, Herzl A, Neumann S, Argiriou A, Vitale D, Liguori R, Piravandi E, Massenet O, Quigley F, Clabauld G, Mündlein A, Felber R, Schnabl S, Hiller R, Schmidt W, Lecharny A, Aubourg S, Chefdor F, Cooke R, Berger C, Montfort A, Casacuberta E, Gibbons T, Weber N, Vandenbol M, Bargues M, Terol J, Torres A, Perez-Perez A, Purnelle B, Bent E, Johnson S, Tacon D, Jesse T, Heijnen L, Schwarz S, Scholler P, Heber S, Francs P, Bielke C, Frishman D, Haase D, Lemcke K, Mewes HW, Stocker S, Zaccaria P, Bevan M, Wilson RK, de la Bastide M, Habermann K, Parnell L, Dedhia N, Gnoj L, Schutz K, Huang E, Spiegel L, Sehkon M, Murray J, Sheet P, Cordes M, Abu-Threideh J, Stoneking T, Kalicki J, Graves T, Harmon G, Edwards J, Latreille P, Courtney L, Cloud J, Abbott A, Scott K, Johnson D, Minx P, Bentley D, Fulton B, Miller N, Greco T, Kemp K, Kramer J, Fulton L, Mardis E, Dante M, Pepin K, Hillier L, Nelson J, Spieth J, Ryan E, Andrews S, Geisel C, Layman D, Du H, Ali J, Berghoff A, Jones K, Drone K, Cotton M, Joshu C, Antonoiu B, Zidanic M, Strong C, Sun H, Lamar B, Yordan C, Ma P, Zhong J, Preston R, Vil D, Shekher M, Matero A, Shah R, Swaby IK, O'Shaughnessy A, Rodriguez M, Hoffmann J, Till S, Granat S, Shohdy N, Hasegawa A, Hameed A, Lodhi M, Johnson A, Chen E, Marra M, Martienssen R, McCombie WR. (1999)
Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana
Nature 402(6763):769-777. doi:10.1038/47134
Europe PMC | doi

Kalousová A, Benes V, Paces J, Paces V, Kozmik Z. (1999)
DNA binding and transactivating properties of the paired and homeobox protein Pax4
Biochem. Biophys. Res. Commun. 259(3):510-518. doi:10.1006/bbrc.1999.0809
Europe PMC | doi