Staff at EMBL

Dr. Vladimir Benes

Head of Genomics Core Facility
Genomics Core Facility

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

E-mail:	send a mail

Biography

PhD 1994, Czech Academy of Sciences, Prague.
Postdoctoral research at EMBL.
Facility head since 2001.

Publications

An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Wilkening, S., Pelechano, V., Jarvelin, A.I., Tekkedil, M.M., Anders, S., Benes, V. & Steinmetz, L.M. Nucleic Acids Res. 2013 Mar 1;41(5):e65. doi: 10.1093/nar/gks1249. Epub 2013 Jan7. PubMed

Disruption of EXOC6B in a patient with developmental delay, epilepsy, and a de novo balanced t(2;8) translocation. Fruhmesser, A., Blake, J., Haberlandt, E., Baying, B., Raeder, B., Runz, H., Spreiz, A., Fauth, C., Benes, V., Utermann, G., Zschocke, J. & Kotzot, D. Eur J Hum Genet. 2013 Feb 20. doi: 10.1038/ejhg.2013.18. PubMed

Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Weischenfeldt, J., Simon, R., Feuerbach, L., Schlangen, K., Weichenhan, D., Minner, S., Wuttig, D., Warnatz, H.J., Stehr, H., Rausch, T., Jager, N., Gu, L., Bogatyrova, O., Stutz, A.M., Claus, R., Eils, J., Eils, R., Gerhauser, C., Huang, P.H., Hutter, B., Kabbe, R., Lawerenz, C., Radomski, S., Bartholomae, C.C., Falth, 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., Sultmann, H., Sauter, G., Plass, C., Brors, B., Yaspo, M.L., Korbel, J.O. & Schlomm, T. Cancer Cell. 2013 Feb 11;23(2):159-70. doi: 10.1016/j.ccr.2013.01.002. PubMed

Df31 Protein and snoRNAs Maintain Accessible Higher-Order Structures of Chromatin. Schubert, T., Pusch, M.C., Diermeier, S., Benes, V., Kremmer, E., Imhof, A. & Langst, G. Mol Cell. 2012 Nov 9;48(3):434-44. doi: 10.1016/j.molcel.2012.08.021. Epub 2012Sep 27. PubMed

A Role for Fkbp6 and the Chaperone Machinery in piRNA Amplification and Transposon Silencing. 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, R.S. Mol Cell. 2012 Sep 28;47(6):970-9. doi: 10.1016/j.molcel.2012.07.019. Epub 2012Aug 16. PubMed

DELLY: structural variant discovery by integrated paired-end and split-read analysis. Rausch, T., Zichner, T., Schlattl, A., Stutz, A.M., Benes, V. & Korbel, J.O. Bioinformatics. 2012 Sep 15;28(18):i333-i339. PubMed

RNA-sequencing as useful screening tool in the combat against the misuse of anabolic agents. Riedmaier, I., Benes, V., Blake, J., Bretschneider, N., Zinser, C., Becker, C., Meyer, H.H. & Pfaffl, M.W. Anal Chem. 2012 Aug 7;84(15):6863-8. Epub 2012 Jul 13. PubMed

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing. Preussner, M., Schreiner, S., Hung, L.H., Porstner, M., Jack, H.M., Benes, V., Ratsch, G. & Bindereif, A. Nucleic Acids Res. 2012 Jul 1;40(12):5666-78. Epub 2012 Mar 8. PubMed

Hfe deficiency impairs pulmonary neutrophil recruitment in response to inflammation. Benesova, K., Vujic Spasic, M., Schaefer, S.M., Stolte, J., Baehr-Ivacevic, T., Waldow, K., Zhou, Z., Klingmueller, U., Benes, V., Mall, M.A. & Muckenthaler, M.U. PLoS One. 2012;7(6):e39363. doi: 10.1371/journal.pone.0039363. Epub 2012 Jun 21. PubMed

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Kahramanoglou, C., Prieto, A.I., Khedkar, S., Haase, B., Gupta, A., Benes, V., Fraser, G.M., Luscombe, N.M. & Seshasayee, A.S. Nat Commun. 2012 Jun 6;3:886. doi: 10.1038/ncomms1878. PubMed

Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway. Simpson, J.C., Joggerst, B., Laketa, V., Verissimo, F., Cetin, C., Erfle, H., Bexiga, M.G., Singan, V.R., Heriche, J.K., Neumann, B., Mateos, A., Blake, J., Bechtel, S., Benes, V., Wiemann, S., Ellenberg, J. & Pepperkok, R. Nat Cell Biol. 2012 Jun 3;14(7):764-74. doi: 10.1038/ncb2510. PubMed

Role of CXCL13 in asthma: novel therapeutic target. Baay-Guzman, G.J., Huerta-Yepez, S., Vega, M.I., Aguilar-Leon, D., Campillos, M., Blake, J., Benes, V., Hernandez-Pando, R. & Teran, L.M. Chest. 2012 Apr;141(4):886-94. doi: 10.1378/chest.11-0633. Epub 2011 Oct 20. PubMed

Direct regulation of microRNA biogenesis and expression by estrogen receptor beta in hormone-responsive breast cancer. Paris, O., Ferraro, L., Grober, O.M., Ravo, M., De Filippo, M.R., Giurato, G., Nassa, G., Tarallo, R., Cantarella, C., Rizzo, F., Di Benedetto, A., Mottolese, M., Benes, V., Ambrosino, C., Nola, E. & Weisz, A. Oncogene. 2012 Jan 9. doi: 10.1038/onc.2011.583. PubMed

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations. Rausch, T., Jones, D.T., Zapatka, M., Stutz, A.M., Zichner, T., Weischenfeldt, J., Jager, N., Remke, M., Shih, D., Northcott, P.A., 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, A.E., Witt, O., Martin, D., Zhang, C., Porat, R., Merino, D.M., Wasserman, J., Jabado, N., Fontebasso, A., Bullinger, L., Rucker, F.G., Dohner, K., Dohner, H., Koster, J., Molenaar, J.J., Versteeg, R., Kool, M., Tabori, U., Malkin, D., Korshunov, A., Taylor, M.D., Lichter, P., Pfister, S.M. & Korbel, J.O. Cell. 2012 Jan 20;148(1-2):59-71. PubMed

Kaposi's Sarcoma Herpesvirus microRNAs Target Caspase 3 and Regulate Apoptosis. Suffert, G., Malterer, G., Hausser, J., Viiliainen, J., Fender, A., Contrant, M., Ivacevic, T., Benes, V., Gros, F., Voinnet, O., Zavolan, M., Ojala, P.M., Haas, J.G. & Pfeffer, S. PLoS Pathog. 2011 Dec;7(12):e1002405. Epub 2011 Dec 8. PubMed

Iron regulatory protein-1 and -2: transcriptome-wide definition of binding mRNAs and shaping of the cellular proteome by iron regulatory proteins. Sanchez, M., Galy, B., Schwanhaeusser, B., Blake, J., Bahr-Ivacevic, T., Benes, V., Selbach, M., Muckenthaler, M.U. & Hentze, M.W. Blood. 2011 Nov 24;118(22):e168-79. Epub 2011 Sep 22. PubMed

Nuclear hormone 1alpha,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy. Heikkinen, S., Vaisanen, S., Pehkonen, P., Seuter, S., Benes, V. & Carlberg, C. Nucleic Acids Res. 2011 Nov 1;39(21):9181-93. Epub 2011 Aug 16. PubMed

Exome sequencing identifies MRPL3 mutation in mitochondrial cardiomyopathy. Galmiche, L., Serre, V., Beinat, M., Assouline, Z., Lebre, A.S., Chretien, D., Nietschke, P., Benes, V., Boddaert, N., Sidi, D., Brunelle, F., Rio, M., Munnich, A. & Rotig, A. Hum Mutat. 2011 Nov;32(11):1225-31. doi: 10.1002/humu.21562. Epub 2011 Sep14. PubMed

Primer Sequence Disclosure: A Clarification of the MIQE Guidelines. Bustin, S.A., Benes, V., Garson, J.A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M.W., Shipley, G.L., Vandesompele, J. & Wittwer, C.T. Clin Chem. 2011 Jun;57(6):919-21. Epub 2011 Mar 18. PubMed

RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation. Rosel, T.D., Hung, L.H., Medenbach, J., Donde, K., Starke, S., Benes, V., Ratsch, G. & Bindereif, A. EMBO J. 2011 May 18;30(10):1965-76. Epub 2011 Apr 5. PubMed

The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice. Castoldi, M., Vujic Spasic, M., Altamura, S., Elmen, J., Lindow, M., Kiss, J., Stolte, J., Sparla, R., D'Alessandro, L.A., Klingmuller, U., Fleming, R.E., Longerich, T., Grone, H.J., Benes, V., Kauppinen, S., Hentze, M.W. & Muckenthaler, M.U. J Clin Invest. 2011 Apr;121(4):1386-96. doi: 10.1172/JCI44883. PubMed

Differentially expressed genes associated with human limbal epithelial phenotypes: new molecules that potentially facilitate selection of stem cell-enriched populations. Takacs, L., Toth, E., Losonczy, G., Szanto, A., Bahr-Ivacevic, T., Benes, V., Berta, A. & Vereb, G. Invest Ophthalmol Vis Sci. 2011 Mar 10;52(3):1252-60. doi: 10.1167/iovs.10-5242. PubMed

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Kahramanoglou, C., Seshasayee, A.S., Prieto, A.I., Ibberson, D., Schmidt, S., Zimmermann, J., Benes, V., Fraser, G.M. & Luscombe, N.M. Nucleic Acids Res. 2011 Mar;39(6):2073-91. doi: 10.1093/nar/gkq934. Epub 2010 Nov21. PubMed

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation. Grober, O.M., Mutarelli, M., Giurato, G., Ravo, M., Cicatiello, L., De Filippo, M.R., Ferraro, L., Nassa, G., Papa, M.F., Paris, O., Tarallo, R., Luo, S., Schroth, G.P., Benes, V. & Weisz, A. BMC Genomics. 2011 Jan 14;12:36. doi: 10.1186/1471-2164-12-36. PubMed

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors. Corbo, J.C., Lawrence, K.A., Karlstetter, M., Myers, C.A., Abdelaziz, M., Dirkes, W., Weigelt, K., Seifert, M., Benes, V., Fritsche, L.G., Weber, B.H. & Langmann, T. Genome Res. 2010 Nov;20(11):1512-25. Epub 2010 Aug 6. PubMed

Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available. Benes, V. & Castoldi, M. Methods. 2010 Apr;50(4):244-9. doi: 10.1016/j.ymeth.2010.01.026. Epub 2010 Jan28. PubMed

Thyrotroph embryonic factor regulates light-induced transcription of repair genes in zebrafish embryonic cells. Gavriouchkina, D., Fischer, S., Ivacevic, T., Stolte, J., Benes, V. & Dekens, M.P. PLoS One. 2010 Sep 7;5(9):e12542. PubMed

Analysis of microribonucleic acid expression by quantitative real-time polymerase chain reaction. Benes, V., Stolte, J., Ibberson, D., Castoldi, M., Muckenthaler, M. In The PCR Revolution: Basic Technologies and Applications (S. Bustin, Ed.) Cambridge Univ Press (2010), ISBN: 978-0-521-88231-6.

An assessment of air as a source of DNA contamination encountered when performing PCR. Witt, N., Rodger, G., Vandesompele, J., Benes, V., Zumla, A., Rook, G.A. & Huggett, J.F. J Biomol Tech. 2009 Dec;20(5):236-40. PubMed

Widespread estrogen-dependent repression of micrornas involved in breast tumor cell growth. Maillot, G., Lacroix-Triki, M., Pierredon, S., Gratadou, L., Schmidt, S., Benes, V., Roche, H., Dalenc, F., Auboeuf, D., Millevoi, S. & Vagner, S. Cancer Res. 2009 Nov 1;69(21):8332-40. Epub 2009 Oct 13. PubMed

Inhibition of aurora kinases for tailored risk-adapted treatment of multiple myeloma. Hose, D., Reme, T., Meissner, T., Moreaux, J., Seckinger, A., Lewis, J.D., Benes, V., Benner, A., Hundemer, M., Hielscher, T., Shaughnessy JD, J.r, Barlogie, B., Neben, K., Kramer, A., Hillengass, J., Bertsch, U., Jauch, A., De Vos, J., Rossi, J.F., Mohler, T., Blake, J., Zimmermann, J., Klein, B. & Goldschmidt, H. Blood. 2009 Apr 30;113(18):4331-40. Epub 2009 Jan 26. PubMed

The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Bustin, S.A., Benes, V., Garson, J.A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M.W., Shipley, G.L., Vandesompele, J. & Wittwer, C.T. Clin Chem. 2009 Apr;55(4):611-22. Epub 2009 Feb 26. PubMed

Unreliable real-time PCR analysis of human endogenous retrovirus-W (HERV-W) RNA expression and DNA copy number in multiple sclerosis. Garson, J.A., Huggett, J.F., Bustin, S.A., Pfaffl, M.W., Benes, V., Vandesompele, J. & Shipley, G.L. AIDS Res Hum Retroviruses. 2009 Mar;25(3):377-8; author reply 379-81. PubMed

Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Weinmann, L., Hock, J., Ivacevic, T., Ohrt, T., Mutze, J., Schwille, P., Kremmer, E., Benes, V., Urlaub, H. & Meister, G. Cell. 2009 Feb 6;136(3):496-507. Epub 2009 Jan 22. PubMed

Aging and replicative senescence have related effects on human stem and progenitor cells. Wagner, W., Bork, S., Horn, P., Krunic, D., Walenda, T., Diehlmann, A., Benes, V., Blake, J., Huber, F.X., Eckstein, V., Boukamp, P. & Ho, A.D. PLoS One. 2009 Jun 9;4(6):e5846. PubMed

MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer. Lowery, A.J., Miller, N., Devaney, A., McNeill, R.E., Davoren, P.A., Lemetre, C., Benes, V., Schmidt, S., Blake, J., Ball, G. & Kerin, M.J. Breast Cancer Res. 2009;11(3):R27. Epub 2009 May 11. PubMed

RNA degradation compromises the reliability of microRNA expression profiling. Ibberson, D., Benes, V., Muckenthaler, M.U. & Castoldi, M. BMC Biotechnol. 2009 Dec 21;9:102. PubMed

Cyclical DNA methylation of a transcriptionally active promoter. Metivier, R., Gallais, R., Tiffoche, C., Le Peron, C., Jurkowska, R.Z., Carmouche, R.P., Ibberson, D., Barath, P., Demay, F., Reid, G., Benes, V., Jeltsch, A., Gannon, F. & Salbert, G. Nature. 2008 Mar 6;452(7183):45-50. PubMed

Transient cyclical methylation of promoter DNA. Kangaspeska, S., Stride, B., Metivier, R., Polycarpou-Schwarz, M., Ibberson, D., Carmouche, R.P., Benes, V., Gannon, F. & Reid, G. Nature. 2008 Mar 6;452(7183):112-5. PubMed

Diverse roles of hnRNP L in mammalian mRNA processing: a combined microarray and RNAi analysis. Hung, L.H., Heiner, M., Hui, J., Schreiner, S., Benes, V. & Bindereif, A. RNA. 2008 Feb;14(2):284-96. Epub 2007 Dec 11. PubMed

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. Denger, S., Bahr-Ivacevic, T., Brand, H., Reid, G., Blake, J., Seifert, M., Lin, C.Y., May, K., Benes, V., Liu, E.T. & Gannon, F. Mol Endocrinol. 2008 Feb;22(2):361-79. Epub 2007 Oct 25. PubMed

Replicative senescence of mesenchymal stem cells: a continuous and organized process. Wagner, W., Horn, P., Castoldi, M., Diehlmann, A., Bork, S., Saffrich, R., Benes, V., Blake, J., Pfister, S., Eckstein, V. & Ho, A.D. PLoS ONE. 2008 May 21;3(5):e2213. PubMed

miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes. Castoldi, M., Schmidt, S., Benes, V., Hentze, M.W. & Muckenthaler, M.U. Nat Protoc. 2008;3(2):321-9. PubMed

miChip: a microarray platform for expression profiling of microRNAs based on locked nucleic acid (LNA) oligonucleotide capture probes. Castoldi, M., Benes, V., Hentze, M.W. & Muckenthaler, M.U. Methods. 2007 Oct;43(2):146-52. PubMed

Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster. Koutsos, A.C., Blass, C., Meister, S., Schmidt, S., MacCallum, R.M., Soares, M.B., Collins, F.H., Benes, V., Zdobnov, E., Kafatos, F.C. & Christophides, G.K. Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11304-9. Epub 2007 Jun 11. PubMed

Pax-Six-Eya-Dach network during amphioxus development: conservation in vitro but context specificity in vivo. Kozmik, Z., Holland, N.D., Kreslova, J., Oliveri, D., Schubert, M., Jonasova, K., Holland, L.Z., Pestarino, M., Benes, V. & Candiani, S. Dev Biol. 2007 Jun 1;306(1):143-59. Epub 2007 Mar 13. PubMed

Adhesion of hematopoietic progenitor cells to human mesenchymal stem cells as a model for cell-cell interaction. Wagner, W., Wein, F., Roderburg, C., Saffrich, R., Faber, A., Krause, U., Schubert, M., Benes, V., Eckstein, V., Maul, H. & Ho, A.D. Exp Hematol. 2007 Feb;35(2):314-25. PubMed

Molecular composition of cell-cell contact between hematopoietic stem cells and mesenchymal stem cells. Wagner, W; Wein, F; Roderburg, C; Benes, V.; Frankhauser, M; Wuchter, P; Eckstein, V; Ho, AD Biology of blood and marrow transplantation February 2007 13(2)

Modular Proteins from the Drosophila sallimus (sls) Gene and their Expression in Muscles with Different Extensibility. Burkart, C., Qiu, F., Brendel, S., Benes, V., Haag, P., Labeit, S., Leonard, K. & Bullard, B. J Mol Biol. 2007 Jan 27;. PubMed

A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). Castoldi, M., Schmidt, S., Benes, V., Noerholm, M., Kulozik, A.E., Hentze, M.W. & Muckenthaler, M.U. RNA. 2006 May;12(5):913-20. Epub 2006 Mar 15. PubMed

The molecular elasticity of the insect flight muscle proteins projectin and kettin. Bullard, B., Garcia, T., Benes, V., Leake, M.C., Linke, W.A. & Oberhauser, A.F. Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4451-6. Epub 2006 Mar 14. PubMed

Adhesion of hematopoietic progenitor cells to hurnan mesenchymal stromal cells as a model for interaction between stem cells and their niche. Wagner, Wolfgang; Wein, Frederik; Roderburg, Christoph; Benes, V., Diehlmann, Anke; Krause, Ulf; Frankhauser, Maria; Wuchter, Patrick; Volker, Eckstein; Ho, Anthony D. Blood November 2006 108(11)

Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii. 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. Science 2005 Nov 25;310(5752):1325-6. PubMed

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. Reid, G., Metivier, R., Lin, C.Y., Denger, S., Ibberson, D., Ivacevic, T., Brand, H., Benes, V., Liu, E.T. & Gannon, F. Oncogene 2005 Jul 21;24(31):4894-907. PubMed

Quantitative real-time RT-PCR - a perspective. Bustin, S.A., Benes, V., Nolan, T. & Pfaffl, M.W. J Mol Endocrinol 2005 Jun;34(3):597-601. PubMed

Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells. Relogio, A., Ben-Dov, C., Baum, M., Ruggiu, M., Gemund, C., Benes, V., Darnell, R.B. & Valcarcel, J. J Biol Chem 2005 Feb 11;280(6):4779-84. Epub 2004 Nov 16. PubMed

Transcriptional complexes engaged by apo-estrogen receptor-alpha isoforms have divergent outcomes. Metivier, R., Penot, G., Carmouche, R.P., Hubner, M.R., Reid, G., Denger, S., Manu, D., Brand, H., Kos, M., Benes, V. & Gannon, F. EMBO J 2004 Sep 15;23(18):3653-66. Epub 2004 Sep 02. PubMed

Characterization of an Escherichia coli elaC deletion mutant. Schilling, O., Ruggeberg, S., Vogel, A., Rittner, N., Weichert, S., Schmidt, S., Doig, S., Franz, T., Benes, V., Andrews, S.C., Baum, M. & Meyer-Klaucke, W. Biochem Biophys Res Commun 2004 Aug 6;320(4):1365-73. PubMed

Targeted mutagenesis of the murine IRP1 and IRP2 genes reveals context-dependent RNA processing differences in vivo. Galy, B., Ferring, D., Benesova, M., Benes, V. & Hentze, M.W. RNA 2004 Jul;10(7):1019-25. PubMed

Diversity of vertebrate splicing factor U2AF35: identification of alternatively spliced U2AF1 mRNAS. Pacheco, T.R., Gomes, A.Q., Barbosa-Morais, N.L., Benes, V., Ansorge, W., Wollerton, M., Smith, C.W., Valcarcel, J. & Carmo-Fonseca, M. J Biol Chem. 2004 Jun 25;279(26):27039-49. Epub 2004 Apr 19. PubMed

Developmentally regulated switching of titin size alters myofibrillar stiffness in the perinatal heart. Opitz, C.A., Leake, M.C., Makarenko, I., Benes, V. & Linke, W.A. Circ Res. 2004 Apr 16;94(7):967-75. Epub 2004 Feb 26. PubMed

BAC engineering for the generation of ES cell-targeting constructs and mouse transgenes. Testa, G., Vintersten, K., Zhang, Y., Benes, V., Muyrers, J.P. & Stewart, A.F. Methods Mol Biol. 2004;256:123-39. PubMed

ET recombination: DNA engineering using homologous recombination in E. coli. Muyrers, J.P., Zhang, Y., Benes, V., Testa, G., Rientjes, J.M. & Stewart, A.F. Methods Mol Biol 2004;256:107-21. PubMed

Microcontact printing of DNA molecules Lange S, Benes V, Kern DP, Hoerber JKH, Bernard A AnalyticalBiochem. (2004), 76, 1641-1647, doi: 10.1021/ac035127w.

Standardization of protocols in cDNA microarray analysis. Benes, V. & Muckenthaler, M. Trends Biochem Sci 2003 May;28(5):244-9. PubMed

Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles. Testa, G., Zhang, Y., Vintersten, K., Benes, V., Pijnappel, W.W., Chambers, I., Smith, A.J., Smith, A.G. & Stewart, A.F. Nat Biotechnol 2003 Apr;21(4):443-7. PubMed

Cloning and developmental expression of amphioxus Dachschund. Candiani, S., Kreslova, J., Benes, V., Oliveri, D., Castagnola, P., Pestarino, M. & Kozmik, Z. Gene Expr Patterns 2003 Mar;3(1):65-9. PubMed

Automatisierte DNA-Extraktion durch Kombination von Liquid Handling und
Zentrifugation Zimmermann, J., Zinn, T., Benes, V., Ibberson, D., Boulin, C., Griebel, R., Lomax, P., Mausel, M., Schubell, U. & Gunther-Eberle, K. Laborwelt 2003 4(5) 41-42

Small is beautiful: Flexible Automatisierunginsel in der genomischen Forschung. Zimmermann, J., Schmidt, S., Benes, V., Boulin, C., Griebel, R., Lomax, P., Zinn, T., Mausel, M., Schubell, U. & Gunther-Eberle, K. Biospektrum 2003 9 764-766

Large BAC-based targeting constructs present new options for genomic engineering. Testa G, Zhang Y, Vintersten K, Benes V, Chambers I, Pim Pijnappel WWM, Smith AJH, Smith AA and Stewart AF Nature Biotech. (2003), 21, 443-7.

The genome sequence of the malaria mosquito Anopheles gambiae. Holt, R.A., Subramanian, G.M., Halpern, A., Sutton, G.G., Charlab, R., Nusskern, D.R., Wincker, P., Clark, A.G., Ribeiro, J.M., Wides, R., Salzberg, S.L., Loftus, B., Yandell, M., Majoros, W.H., Rusch, D.B., Lai, Z., Kraft, C.L., Abril, J.F., Anthouard, V., Arensburger, P., Atkinson, P.W., Baden, H., de Berardinis, V., Baldwin, D., Benes, V., Biedler, J., Blass, C., Bolanos, R., Boscus, D., Barnstead, M., Cai, S., Center, A., Chatuverdi, K., Christophides, G.K., Chrystal, M.A., Clamp, M., Cravchik, A., Curwen, V., Dana, A., Delcher, A., Dew, I., Evans, C.A., Flanigan, M., Grundschober-Freimoser, A., Friedli, L., Gu, Z., Guan, P., Guigo, R., Hillenmeyer, M.E., Hladun, S.L., Hogan, J.R., Hong, Y.S., Hoover, J., Jaillon, O., Ke, Z., Kodira, C., Kokoza, E., Koutsos, A., Letunic, I., Levitsky, A., Liang, Y., Lin, J.J., Lobo, N.F., Lopez, J.R., Malek, J.A., McIntosh, T.C., Meister, S., Miller, J., Mobarry, C., Mongin, E., Murphy, S.D., O'Brochta, D.A., Pfannkoch, C., Qi, R., Regier, M.A., Remington, K., Shao, H., Sharakhova, M.V., Sitter, C.D., Shetty, J., Smith, T.J., Strong, R., Sun, J., Thomasova, D., Ton, L.Q., Topalis, P., Tu, Z., Unger, M.F., Walenz, B., Wang, A., Wang, J., Wang, M., Wang, X., Woodford, K.J., Wortman, J.R., Wu, M., Yao, A., Zdobnov, E.M., Zhang, H., Zhao, Q., Zhao, S., Zhu, S.C., Zhimulev, I., Coluzzi, M., della Torre, A., Roth, C.W., Louis, C., Kalush, F., Mural, R.J., Myers, E.W., Adams, M.D., Smith, H.O., Broder, S., Gardner, M.J., Fraser, C.M., Birney, E., Bork, P., Brey, P.T., Venter, J.C., Weissenbach, J., Kafatos, F.C., Collins, F.H. & Hoffman, S.L. Science 2002 Oct 4;298(5591):129-49. PubMed

A genomic switch at the transition from cell proliferation to terminal differentiation in the Drosophila eye. Jasper, H., Benes, V., Atzberger, A., Sauer, S., Ansorge, W. & Bohmann, D. Dev Cell 2002 Oct;3(4):511-21. PubMed

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. Krelova, J., Holland, L.Z., Schubert, M., Burgtorf, C., Benes, V. & Kozmik, Z. Gene 2002 Jan 9;282(1-2):143-50. PubMed

The genomic response of the Drosophila embryo to JNK signaling. Jasper, H., Benes, V., Schwager, C., Sauer, S., Clauder-Munster, S., Ansorge, W. & Bohmann, D. Dev Cell 2001 Oct;1(4):579-86. PubMed

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Salanoubat, M., Lemcke, K., Rieger, M., Ansorge, W., Unseld, M., Fartmann, B., Valle, G., Blocker, H., Perez-Alonso, M., Obermaier, B., Delseny, M., Boutry, M., Grivell, L.A., Mache, R., Puigdomenech, P., De Simone, V., Choisne, N., Artiguenave, F., Robert, C., Brottier, P., Wincker, P., Cattolico, L., Weissenbach, J., Saurin, W., Quetier, F., Schafer, M., Muller-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., Lohnert, T.H., Nordsiek, G., Reichelt, J., Scharfe, M., Schon, O., Bargues, M., Terol, J., Climent, J., Navarro, P., Collado, C., Perez-Perez, A., Ottenwalder, B., Duchemin, D., Cooke, R., Laudie, M., Berger-Llauro, C., Purnelle, B., Masuy, D., de Haan, M., Maarse, A.C., Alcaraz, J.P., 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, H.W., Mayer, K.F., Kaul, S., Town, C.D., Koo, H.L., Tallon, L.J., Jenkins, J., Rooney, T., Rizzo, M., Walts, A., Utterback, T., Fujii, C.Y., Shea, T.P., Creasy, T.H., Haas, B., Maiti, R., Wu, D., Peterson, J., Van Aken, S., Pai, G., Militscher, J., Sellers, P., Gill, J.E., Feldblyum, T.V., Preuss, D., Lin, X., Nierman, W.C., Salzberg, S.L., White, O., Venter, J.C., Fraser, C.M., 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. Nature 2000 Dec 14;408(6814):820-2. PubMed

Point mutation of bacterial artificial chromosomes by ET recombination. Muyrers, J.P., Zhang, Y., Benes, V., Testa, G., Ansorge, W. & Stewart, A.F. EMBO Rep. 2000 Sep;1(3):239-43. PubMed

A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation. 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, G.A. Am J Hum Genet 2000 Sep;67(3):563-73. PubMed

An estimate of large-scale sequencing accuracy. Hill, F., Gemund, C., Benes, V., Ansorge, W. & Gibson, T.J. EMBO Rep. 2000 Jul;1(1):29-31. PubMed

Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines. Dimopoulos, G., Casavant, T.L., Chang, S., Scheetz, T., Roberts, C., Donohue, M., Schultz, J., Benes, V., Bork, P., Ansorge, W., Soares, M.B. & Kafatos, F.C. Proc Natl Acad Sci U S A 2000 Jun 6;97(12):6619-24 PubMed

Genetic diversity of Borrelia burgdorferi sensu lato in ticks from mainland Portugal. De Michelis, S., Sewell, H.S., Collares-Pereira, M., Santos-Reis, M., Schouls, L.M., Benes, V., Holmes, E.C. & Kurtenbach, K. J Clin Microbiol 2000 Jun;38(6):2128-33. PubMed

Progress in Arabidopsis genome sequencing and functional genomics. Wambutt, R., Murphy, G., Volckaert, G., Pohl, T., Dusterhoft, A., Stiekema, W., Entian, K.D., Terryn, N., Harris, B., Ansroge, W., Brandt, P., Grivell, L., Rieger, M., Weichselgartner, M., de Simone, V., Obermaier, B., Mache, R., Muller, 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, S.A., McCullagh, B., Bilham, L., Robben, J., Van der Schueren, J., Grymonprez, B., Chuang, Y.J., Vandenbussche, F., Braeken, M., Weltjens, I., Voet, M., Bastiens, I., Aert, R., Defoor, E., Weitzenegger, T., Bothe, G. & Rose, M. J Biotechnol 2000 Mar 31;78(3):281-92. PubMed

Sequence and expression of the kettin gene in drosophila melanogaster and caenorhabditis elegans. Kolmerer, B., Clayton, J., Benes, V., Allen, T., Ferguson, C., Leonard, K., Weber, U., Knekt, M., Ansorge, W., Labeit, S. & Bullard, B. J Mol Biol 2000 Feb 18;296(2):435-48 PubMed

BAC trimming: Minimizing clone overlaps. Hill, F., Benes, V., Thomasova, D., Stewart, A.F., Kafatos, F.C. & Ansorge, W. Genomics 2000 Feb 15;64(1):111-113 PubMed

Genomic locus and promoter region of rat Smad7, an important antagonist of TGFbeta signaling. Stopa, M., Benes, V., Ansorge, W., Gressner, A.M. & Dooley, S. Mamm Genome 2000 Feb;11(2):169-76 PubMed

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Mayer, K., Schuller, C., Wambutt, R., Murphy, G., Volckaert, G., Pohl, T., Dusterhoft, A., Stiekema, W., Entian, K.D., Terryn, N., Harris, B., Ansorge, W., Brandt, P., Grivell, L., Rieger, M., Weichselgartner, M., de Simone, V., Obermaier, B., Mache, R., Muller, M., Kreis, M., Delseny, M., Puigdomenech, P., Watson, M., McCombie, W.R. & et, al Nature 1999 Dec 16;402(6763):769-77 PubMed

Sec61beta, a subunit of the protein translocation channel, is required during Drosophila development. Valcarcel, R., Weber, U., Jackson, D.B., Benes, V., Ansorge, W., Bohmann, D. & Mlodzik, M. J Cell Sci 1999 Dec;112 ( Pt 23):4389-96 PubMed

DNA binding and transactivating properties of the paired and homeobox protein Pax4. Kalousova, A., Benes, V., Paces, J., Paces, V. & Kozmik, Z. Biochem Biophys Res Commun 1999 Jun 16;259(3):510-8. PubMed

Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Kal, A.J., van Zonneveld, A.J., Benes, V., van den Berg, M., Koerkamp, M.G., Albermann, K., Strack, N., Ruijter, J.M., Richter, A., Dujon, B., Ansorge, W. & Tabak, H.F. Mol Biol Cell 1999 Jun;10(6):1859-72 PubMed

Bacteriophage phi29 early protein p17 is conditionally required for the first rounds of viral DNA replication. Crucitti, P., Lazaro, J.M., Benes, V. & Salas, M. Gene 1998 Nov 26;223(1-2):135-42. PubMed

Systematic gain-of-function genetics in Drosophila. Rorth, P., Szabo, K., Bailey, A., Laverty, T., Rehm, J., Rubin, G.M., Weigmann, K., Milan, M., Benes, V., Ansorge, W. & Cohen, S.M. Development 1998 Mar;125(6):1049-57. PubMed

Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana Bevan, M., Bancroft, I., Bent, E., Love, K., Goodman, H., Dean, C., Bergkamp, R., Dirkse, W., Van Staveren, M., Stiekema, W., Drost, L., Ridley, P., Hudson, S.A., Patel, K., Murphy, G., Piffanelli, P., Wedler, H., Wedler, E., Wambutt, R., Weitzenegger, T., Pohl, T.M., Terryn, N., Gielen, J., Villarroel, R., Chalwatzis, N. & et, al Nature 1998 Jan 29 391(6666) 485-488 PubMed

Strawberry vein banding virus--definitive member of the genus Caulimovirus. Petrzik, K., Benes, V., Mraz, I., Honetslegrova-Franova, J., Ansorge, W. & Spak, J. Virus Genes 1998 16(3) 303-305 PubMed

Bacteriophage B103: complete DNA sequence of its genome and relationship to other Bacillus phages. Pecenkova, T., Benes, V., Paces, J., Vlcek, C. & Paces, V. Gene 1997 Oct 15;199(1-2):157-63. PubMed

Automated cycle sequencing with Taquenase: protocols for internal labeling, dye primer and "doublex" simultaneous sequencing. Voss, H., Nentwich, U., Duthie, S., Wiemann, S., Benes, V., Zimmermann, J. & Ansorge, W. Biotechniques 1997 Aug;23(2):312-8 PubMed

Direct primer walking on P1 plasmid DNA. Benes, V., Kilger, C., Voss, H., Paabo, S. & Ansorge, W. Biotechniques 1997 Jul;23(1):98-100 PubMed

DNA sequencing and analysis of 130 kb from yeast chromosome XV. Voss, H., Benes, V., Andrade, M.A., Valencia, A., Rechmann, S., Teodoru, C., Schwager, C., Paces, V., Sander, C. & Ansorge, W. Yeast 1997 Jun 15;13(7):655-72 PubMed

Simultaneous loading of 200 sample lanes for DNA sequencing on vertical and horizontal, standard and ultrathin gels. Erfle, H., Ventzki, R., Voss, H., Rechmann, S., Benes, V., Stegemann, J. & Ansorge, W. Nucleic Acids Res 1997 Jun 1;25(11):2229-30 PubMed

The nucleotide sequence of Saccharomyces cerevisiae chromosome XII. Johnston, M., Hillier, L., Riles, L., Albermann, K., Andre, B., Ansorge, W., Benes, V., Bruckner, M., Delius, H., Dubois, E., Dusterhoft, A., Entian, K.D., Floeth, M., Goffeau, A., Hebling, U., Heumann, K., Heuss-Neitzel, D., Hilbert, H., Hilger, F., Kleine, K., Kotter, P., Louis, E.J., Messenguy, F., Mewes, H.W., Hoheisel, J.D. & et, al Nature 1997 May 29;387(6632 Suppl):87-90 PubMed

The nucleotide sequence of Saccharomyces cerevisiae chromosome XV. Dujon, B., Albermann, K., Aldea, M., Alexandraki, D., Ansorge, W., Arino, J., Benes, V., Bohn, C., Bolotin-Fukuhara, M., Bordonne, R., Boyer, J., Camasses, A., Casamayor, A., Casas, C., Cheret, G., Cziepluch, C., Daignan-Fornier, B., Dang, D.V., de Haan, M., Delius, H., Durand, P., Fairhead, C., Feldmann, H., Gaillon, L., Kleine, K. & et, al Nature 1997 May 29;387(6632 Suppl):98-102 PubMed

The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Bussey, H., Storms, R.K., Ahmed, A., Albermann, K., Allen, E., Ansorge, W., Araujo, R., Aparicio, A., Barrell, B., Badcock, K., Benes, V., Botstein, D., Bowman, S., Bruckner, M., Carpenter, J., Cherry, J.M., Chung, E., Churcher, C., Coster, F., Davis, K., Davis, R.W., Dietrich, F.S., Delius, H., DiPaolo, T., Hani, J. & et, al Nature 1997 May 29;387(6632 Suppl):103-5 PubMed

Molecular characterization of two high affinity sulfate transporters in Saccharomyces cerevisiae. Cherest, H., Davidian, J.C., Thomas, D., Benes, V., Ansorge, W. & Surdin-Kerjan, Y. Genetics 1997 Mar;145(3):627-35 PubMed

System for simultaneous sequencing of 240 clones with 5 dyes, 1300 bases readings (up to 5000 bases per sequence reaction) with novel loading technique for vertical and horizontal standard or ultrathin gels. Stegemann, J., Ventzki, R., Schwager, C., Erfle, H., Benes, V., Voss, H., & Ansorge, W. FASEB J. 1997 11(9)

Sequencing and analysis of 51 kb on the right arm of chromosome XV from Saccharomyces cerevisiae reveals 30 open reading frames. Wiemann, S., Rechmann, S., Benes, V., Voss, H., Schwager, C., Vlcek, C., Stegemann, J., Zimmermann, J., Erfle, H., Paces, V. & Ansorge, W. Yeast 1996 Mar 15;12(3):281-8 PubMed

"Doublex" fluorescent DNA sequencing: two independent sequences obtained simultaneously in one reaction with internal labeling and unlabeled primers. Wiemann, S., Stegemann, J., Zimmermann, J., Voss, H., Benes, V. & Ansorge, W. Anal Biochem 1996 Feb 15;234(2):166-74 PubMed

Sequencing 39,350 bp of Saccharomyces cerevisiae chromosome XII utilizing ordered shotgun libraries. Scholler, P., Benes, V., Voss, H., Ansorge, W. & Hoheisel, J.D. DNA Seq 1996;6(5):257-62 PubMed

Nucleotide sequence analysis of a 30-kb region of the bovine herpesvirus 1 genome which exhibits a colinear gene arrangement with the UL21 to UL4 genes of herpes simplex virus. Vlcek, C., Benes, V., Lu, Z., Kutish, G.F., Paces, V., Rock, D., Letchworth, G.J. & Schwyzer, M. Virology. 1995 Jun 20;210(1):100-8. PubMed

Protein-induced bending or flexing at the 5'-end of the duck beta A-globin promoter. Matlova, R., Horska, K., Benes, V., Cvekl, A. & Sponar, J. Gene. 1995 Apr 24;156(2):277-81. PubMed

M13 and pUC vectors with new unique restriction sites for cloning. Benes, V., Hostomsky, Z., Arnold, L. & Paces, V. Gene. 1993 Aug 16;130(1):151-2. PubMed

Isolation, biochemical characterization and crystallization of the p15gag proteinase of myeloblastosis associated virus expressed in E. coli. Pichova, I., Strop, P., Sedlacek, J., Kapralek, F., Benes, V., Travnicek, M., Pavlickova, L., Soucek, M., Kostka, V. & Foundling, S. Int J Biochem. 1992 Feb;24(2):235-42. PubMed

Nucleotide sequence of the right early region of Bacillus phage phi 15 and comparison with related phages: reorganization of gene 17 during evolution. Benes, V., Arnold, L., Smrt, J. & Paces, V. Gene. 1989 Feb 20;75(2):341-7. PubMed