Selected References

Blake J, Riddell A, Theiss S, Gonzalez AP, Haase B, Jauch A, Janssen JWG, Ibberson D, Pavlinic D, Moog U, Benes V, Runz H: Sequencing of a patient with balanced chromosome abnormalities and neurodevelopmental disease identifies disruption of multiple high risk loci by structural variation. PLoS ONE (2014) in press.
Gupta I, Clauder-Münster S, Klaus B, Järvelin AI, Aiyar RS, Benes V, Wilkening S, Huber W, Pelechano V, Steinmetz LM: Alternative polyadenylation diversifies posttranscriptional regulation by selective RNA-protein interactions. Molecular Systems Biol (2014) accepted.

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: Identification of novel sequence variations in microRNAs in chronic lymphocytic leukemia. Carcinogenesis (2013) doi: 10.1093/carcin/bgt396.
Paakinaho V, Kaikkonen S, Makkonen H, Benes V, Palvimo J: SUMOylation Regulates the Chromatin Occupancy and Anti-Proliferative Gene Programs of Glucocorticoid Receptor. Nucl Acids Res (2013) doi:10.1093/nar/gkt1033.

Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG: Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods 10 (2013) 1093-95.

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: Primate genome architecture influences structural variation mechanisms and functional consequences. Proc Natl Acad Sci U S A 110 (2013) 15764-9.

Bettencourt P, Marion S, Pires D, Santos L, Lastrucci C, Carmo N, Blake J, Benes V, Griffiths G, Neyrolles O, Lugo-Villarino G, Anes E: 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. Frontiers in Cellular and Infection Microbiology 3 (2013) 19, doi: 10.3389/fcimb.2013.00019.

Di Giacomo M, Comazzetto S, Saini H, De Fazio S, Carrieri C, Morgan M, Vasiliauskaite L, Benes V, Enright AJ, O'Carroll D: Multiple Epigenetic Mechanisms and the piRNA Pathway Enforce LINE1 Silencing during Adult Spermatogenesis. Mol Cell 50 (2013) 601-8.

Frühmesser A, Blake J, Haberlandt E, Baying B, Raeder B, Runz H, Spreiz A, Fauth C, Benes V, Utermann G, Zschocke J, Kotzot D: Disruption of EXOC6B in a patient with developmental delay, epilepsy, and a de novo balanced t(2;8) translocation. Eur J Hum Genet 21 (2013) 1177-80.

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: Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell 23 (2013) 159-70.

Wilkening S, Pelechano V, Järvelin A, Tekkedil M, Anders S, Benes V, Steinmetz L: An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Research 41 (2013) e65.
Schubert T, Pusch MC, Diermeier S, Benes V, Kremmer E, Imhof A, Längst G: Df31 Protein and snoRNAs Maintain Accessible Higher-Order Structures of Chromatin. Mol Cell 48 (2012) 434-44.
Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO: DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28 (2012) i333-i339.

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: A Role for Fkbp6 and the Chaperone Machinery in piRNA Amplification and Transposon Silencing. Mol Cell 47 (2012) 970-9.

Riedmaier I, Benes V, Blake J, Bretschneider N, Zinser C, Becker Ch, Meyer H, Pfaffl M: RNA-Sequencing as useful screening tool in the combat against the misuse of anabolic agents. Analytical Chemistry 84 (2012) 6863-8.

Jones DTW, Jäger N, Kool M, Zichner T, Hutter B, Sultan M, Cho Y-J, Pugh T, Hovestadt V, Stütz A, Rausch T, Warnatz H-J, Ryzhova M, Bender D, 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 U, Wang Q, Lasitschka B, Bartholomä C, Schmidt M, von Kalle Ch, Ast V, Lawerenz Ch, Eils1 J, Kabbe R, Benes V, van Sluis P, Koster J, Volckmann R, Shih D, Coco S, Tonini G-P, Schüller U, Hans V, Graf N, Kim Y-J, Monoranu C, Roggendorf W, Unterberg A, Herold-Mende Ch, Milde T, Kulozik AE, von Deimling A, Witt O, Maass E, Ebinger M, Schuhmann MU, Frühwal MC, Hasselblatt M, Jabado N, Rutkowski S, von Büren AO, Williamson D, Clifford SC, McCabe MG, Collins VP, Wolf S, Wiemann S, Lehrach H, Brors B, Scheurlen W, Felsberg J, Reifenberger G, Northcott PO, Taylor MD, Meyerson MLD, Pomeroy SL, Yaspo M-L, Korbel JO, Korshunov A, Eils R, Pfister SM and Lichter P on behalf of the ICGC PedBrain Tumor Project: ICGC PedBrain: Dissecting the genomic complexity underlying medulloblastoma Nature 488 (2012) 100-105.

Benesova K, Spasic MV, Schaefer SM, Stolte J, Bähr-Ivacevic T, Waldow K, Zhou Z, Klingmueller U, Benes V, Mall MA, Muckenthaler MU: Hfe deficiency impairs pulmonary neutrophil recruitment in response to inflammation: PLoS One 7 (2012) e39363.

Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee AS: Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat Commun 3 (2012) 886, doi: 10.1038/ncomms1878.

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. Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway. Nat Cell Biol 14 (2012) 764-74.

Preußner M, Schreiner S, Hung LH, Porstner M, Jäck HM, Benes V, Rätsch G, Bindereif A: HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing. Nucleic Acids Res 40 (2012) 5666-78.
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. Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell 148 (2012) 59-71.

Paris O, Ferraro L, Grober O MV, 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: Direct Regulation of microRNA Biogenesis and Expression by Estrogen Receptor Beta in Hormone-responsive Breast Cancer. Oncogene 31 (2011) 4196-206, doi: 10.1038/onc.2011.583.
Suffert G, Malterer G, Hausser J, Viiliäinen J, Ivacevic T, Benes V, Gros F, Voinnet O, Zavolan M, Ojala PM, Haas J, Pfeffer S: Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis. PLoS Pathogens 7 (2011) e1002405.

Baay-Guzman GJ, Huerta-Yepez S, Vega MI, Aguilar-Leon D, Campillos M, Blake J, Benes V, Hernandez-Pando R, Teran LM: Role of CXCL13 in Allergic Airway Inflammation: Novel Therapeutic Target. Chest 141 (2011) 886-94.

Sanchez M, Galy B, Schwanhaeusser B, Blake J, Bähr-Ivacevic T, Benes V, Selbach M, Muckenthaler MU, Hentze MW: Iron regulatory protein-1 and -2: transcriptome-wide definition of binding mRNAs and shaping of the cellular proteome by IRPs. Blood 118 (2011) e168-e179.

Heikkinen S, Väisänen S, Pehkonen P, Seuter S, Benes V, Carlberg C: Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy. Nucleic Acids Res 39 (2011) 9181-93.

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: Exome sequencing identifies MRPL3 mutation in mitochondrial cardiomyopathy. Hum Mutat 32 (2011) 1225-31.

Rösel TD, Hung LH, Medenbach J, Donde K, Starke S, Benes V, Rätsch G, Bindereif A: RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation. EMBO J 30 (2011) 1965-76.
Castoldi M, Spasic MV, Altamura S, Elmen J, Lindow M, Kiss J, Stolte J, Sparla R, D’Alessandro L, Klingmüller U, Fleming R, Longerich T, Gröne HJ, Benes V, Kauppinen S, Hentze MW, Muckenthaler M: The liver specific microRNA miR-122 controls systemic iron homeostasis in mice. J Clin Investigation 121 (2011) 1386-96.

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: 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 (2011) 36.

Kahramanoglou C, Seshasayee AS, Prieto AI, Ibberson D, Schmidt S, Zimmermann J, Benes V, Fraser GM, Luscombe NM: Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res 39 (2011) 2073-91.

Takacs L, Toth E, Losonczy G, Szanto A, Bähr-Ivacevic T, Benes V, Berta A, Vereb G: 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 (2011) 1252-60.

Gavriouchkina D, Fischer S, Ivacevic T, Stolte J, Benes V, Dekens MP: Thyrotroph embryonic factor regulates light-induced transcription of repair genes in zebrafish embryonic cells. PLoS One 5 (2010) e12542.
Corbo JC, Lawrence KA, Karlstetter M, Myers CA, Abdelaziz M, Dirkes W, Weigelt K, Seifert M, Benes V, Fritsche LG, Weber BH, Langmann T: CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors. Genome Research 20 (2010) 1512-25.

Benes V, Castoldi M: Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available. Methods 50 (2010) 244-9.

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

GC2. Mueller C, Schrag M, Crofton A, Stolte J, Muckenthaler MU, Magaki S, Kirsch W: Altered serum iron and copper homeostasis predicts cognitive decline in mild cognitive impairment. J Alzheimers Dis 29 (2012) 341-50.

GC1. Rodrigues PN, Gomes SS, Neves JV, Gomes-Pereira S, Correia-Neves M, Nunes-Alves C, Stolte J, Sanchez M, Appelberg R, Muckenthaler MU, Gomes MS: Mycobacteria-induced anaemia revisited: a molecular approach reveals the involvement of NRAMP1 and lipocalin-2, but not of hepcidin. Immunobiology 216 (2011) 1127-34.

 

Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available.
Benes, V. & Castoldi, M.
Methods. 2010 Jan 25.
PubMed

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

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

Transcriptome complexity in a genome-reduced bacterium.
Guell M., van Noort V., Yus E., Chen W.-H., Leigh-Bell J., Michalodimitrakis K., Yamada T., Arumugam M., Doerks T., Kuehner S., Rode M., Suyama M., Gavin, A.C., Bork, P. and Serrano L.
Science 2009 326 1268-1271

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

Hfe acts in hepatocytes to prevent hemochromatosis.
Vujic Spasic, M., Kiss, J., Herrmann, T., Galy, B., Martinache, S., Stolte, J., Grone, H.J., Stremmel, W., Hentze, M.W. & Muckenthaler, M.U.
Cell Metab. 2008 Feb;7(2):173-8.
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

Lack of haptoglobin affects iron transport across duodenum by modulating ferroportin expression.
Marro, S., Barisani, D., Chiabrando, D., Fagoonee, S., Muckenthaler, M.U., Stolte, J., Meneveri, R., Haile, D., Silengo, L., Altruda, F. & Tolosano, E.
Gastroenterology. 2007 Oct;133(4):1261-1271.
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

Physiologic systemic iron metabolism in mice deficient for duodenal Hfe.
Spasic, M.V., Kiss, J., Herrmann, T., Kessler, R., Stolte, J., Galy, B., Rathkolb, B., Wolf, E., Stremmel, W., Hentze, M.W. & Muckenthaler, M.U.
Blood. 2007 May 15;109(10):4511-7. Epub 2007 Jan 30.
PubMed

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

STAT3 mediates hepatic hepcidin expression and its inflammatory stimulation.
Verga Falzacappa, M.V., Vujic Spasic, M., Kessler, R., Stolte, J., Hentze, M.W. & Muckenthaler, M.U.
Blood. 2007 Jan 1;109(1):353-8. Epub 2006 Aug 31.
PubMed

Iron regulation and the cell cycle: identification of an iron-responsive element in the 3'-untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy.
Sanchez, M., Galy, B., Dandekar, T., Bengert, P., Vainshtein, Y., Stolte, J., Muckenthaler, M.U. & Hentze, M.W.
J Biol Chem. 2006 Aug 11;281(32):22865-74. Epub 2006 Jun 7.
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, Vladimir; Diehlmann, Anke; Krause, Ulf; Frankhauser, Maria; Wuchter, Patrick; Volker, Eckstein; Ho, Anthony D.
Blood November 2006 108(11)

Proteomic analysis of nasal aspirates derived from children suffering influenza virus infection.
Teran, LM; Ruggeberg, S; Hernandez, JL; Fuentes-Arenas, F; Franz, T
Molecular & Cellular Proteomics October 2006 5(10)

Targeted disruption of the mouse mitoferrin (Slc25A37) mitochondrial solute carrier results in defective primitive and definitive erythropoiesis.
Paw, Barry H.; Gwynn, Babette; Langer, Nathaniel B.; Shaw, George C.; Lambert, Amy J.; Boyer, Leah A.; Li, Liangtao; Stolte, Jens; Robledo, Raymond F.; Sahr, Kenneth E.; Schlaeger, Thorsten M.; Hentze, Matthias W.; Muckenthaler, Martina U.; Kaplan, Jerry; Peters, Luanne L.
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

An Hfe-dependent pathway mediates hyposideremia in response to lipopolysaccharide-induced inflammation in mice.
Roy, C.N., Custodio, A.O., de Graaf, J., Schneider, S., Akpan, I., Montross, L.K., Sanchez, M., Gaudino, A., Hentze, M.W., Andrews, N.C. & Muckenthaler, M.U.
Nat Genet 2004 May;36(5):481-5. Epub 2004 Apr 18.
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

Regulatory defects in liver and intestine implicate abnormal hepcidin and Cybrd1 expression in mouse hemochromatosis.
Muckenthaler, M., Roy, C.N., Custodio, A.O., Minana, B., deGraaf, J., Montross, L.K., Andrews, N.C. & Hentze, M.W.
Nat Genet 2003 May;34(1):102-7.
PubMed

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

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

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