PuSH - Publikationsserver des Helmholtz Zentrums München

Hipp, C. ; Mussgnug, S.* ; Choudhary, P.* ; Kang, H.-S. ; Asami, S. ; Sastre, J.* ; Donau, C.* ; Böttcher, R.* ; Gemmecker, G. ; Boekhoven, J.* ; Förstemann, K.* ; Sattler, M.

Molecular mechanisms of biomolecular condensate formation in Drosophila melanogaster siRNA biogenesis.

Nucleic Acids Res. 53:gkaf664 (2025)

Mianesaz, H.* ; Göczi, L.* ; Nagy, G.* ; Póliska, S.* ; Fadel, L. ; Bojcsuk, D.* ; Penyige, A.* ; Szirák, K.* ; AlHaman, F.* ; Nagy, L.* ; Vámosi, G.* ; Széles, L.*

Genomic regions occupied by both RARα and VDR are involved in the convergence and cooperation of retinoid and vitamin D signaling pathways.

Nucleic Acids Res. 53:gkaf230 (2025)

Müller-Hermes, C. ; Piomponi, V.* ; Hilber, S.* ; Asami, S.* ; Kreutz, C.* ; Bussi, G.* ; Sattler, M.

Unique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA.

Nucleic Acids Res. 53:gkaf550 (2025)

Pérez-Ràfols, A.* ; Pérez-Ropero, G.* ; Cerofolini, L.* ; Sperotto, L. ; Roca-Martínez, J.* ; Higuera-Rodriguez, R.A.* ; Russomanno, P.* ; Kaiser, W.J.* ; Vranken, W.F.* ; Danielson, U.H.* ; Provenzani, A.* ; Martelli, T.* ; Sattler, M. ; Buijs, J.* ; Fragai, M.*

Deciphering the RNA recognition by Musashi-1 to design protein and RNA variants for in vitro and in vivo applications.

Nucleic Acids Res. 53:gkaf741 (2025)

Schmdit, T. ; Wiesbeck, M. ; Egert, L. ; Truong, T.-T. ; Danese, A.* ; Voshagen, L.* ; Imhof, S.* ; Iraci Borgia, M.* ; Deeksha ; Neuner, A.M. ; Köferle, A. ; Geerlof, A. ; Mourao, A. ; Stricker, S.H.

Efficient DNA- and virus-free engineering of cellular transcriptomic states using dCas9 ribonucleoprotein (dRNP) complexes.

Nucleic Acids Res. 53:gkaf235 (2025)

Steinkamp, R. ; Tsitsiridis, G. ; Brauner, B. ; Montrone, C. ; Fobo, G. ; Frishman, G. ; Avram, S.* ; Oprea, T.I.* ; Ruepp, A.

CORUM in 2024: Protein complexes as drug targets.

Nucleic Acids Res. 53, D651-D657 (2025)

Vilov, S. ; Heinig, M.

Investigating the performance of foundation models on human 3'UTR sequences.

Nucleic Acids Res. 53:gkaf871 (2025)

Werner, M. ; Trauner, M. ; Schauer, T. ; Ummethum, H. ; Márquez-Gómez, E. ; Lalonde, M. ; Lee, C.S.K. ; Tsirkas, I. ; Sajid, A. ; Murriello, A.C. ; Längst, G.* ; Hamperl, S.

Transcription-replication conflicts drive R-loop-dependent nucleosome eviction and require DOT1L activity for transcription recovery.

Nucleic Acids Res. 53:gkaf109 (2025)

Kiss, A.E.* ; Venkatasubramani, A.V.* ; Pathirana, D.* ; Krause, S.* ; Sparr, A.C.* ; Hasenauer, J. ; Imhof, A.* ; Müller, M.* ; Becker, P.B.*

Processivity and specificity of histone acetylation by the male-specific lethal complex.

Nucleic Acids Res. 52, 4889-4905 (2024)

Kuhn, C.K.* ; Stenzel, U.* ; Berndt, S.I* ; Liebscher, I.* ; Schöneberg, T.* ; Horn, S.

The repertoire and structure of adhesion GPCR transcript variants assembled from publicly available deep-sequenced human samples.

Nucleic Acids Res. 52, 3823-3836 (2024)

Luzak, V.* ; Osses, E.* ; Danese, A. ; Odendaal, C.* ; Cosentino, R.O.* ; Stricker, S.H. ; Haanstra, J.R.* ; Erhard, F.* ; Siegel, T.N.*

SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes.

Nucleic Acids Res., DOI: 10.1093/nar/gkae1203 (2024)

Matsuda, A.* ; Plewka, J.* ; Rawski, M.* ; Mourao, A. ; Zajko, W.* ; Siebenmorgen, T. ; Kresik, L.* ; Lis, K.* ; Jones, A. ; Pachota, M.* ; Karim, A.* ; Hartman, K.* ; Nirwal, S.* ; Sonani, R.* ; Chykunova, Y.* ; Minia, I.* ; Mak, P.* ; Landthaler, M.* ; Nowotny, M.* ; Dubin, G.* ; Sattler, M. ; Suder, P.* ; Popowicz, G.M. ; Pyrc, K.* ; Czarna, A.*

Despite the odds: Formation of the SARS-CoV-2 methylation complex.

Nucleic Acids Res. 52, 6441-6458 (2024)

Niedner, A. ; Monecke, T.* ; Hennig, J. ; Klostermann, M.* ; Hofweber, M.* ; Davydova, E.-O. ; Gerber, A.P.* ; Anosova, I. ; Mayer, W.* ; Müller, M. ; Heym, R.G. ; Janowski, R. ; Paillart, J.C.* ; Dormann, D.* ; Zarnack, K.* ; Sattler, M. ; Niessing, D.

Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation.

Nucleic Acids Res. 52, 14205-14228 (2024)

Perez, G.* ; Barber, G.P.* ; Benet-Pages, A. ; Casper, J.* ; Clawson, H.* ; Diekhans, M.* ; Fischer, C.* ; Gonzalez, J.N.* ; Hinrichs, A.S.* ; Lee, C.M.* ; Nassar, L.R.* ; Raney, B.J.* ; Speir, M.L.* ; van Baren, M.J.* ; Vaske, C.J.* ; Haussler, D.* ; Kent, W.J.* ; Haeussler, M.*

The UCSC Genome Browser database: 2025 update.

Nucleic Acids Res., DOI: 10.1093/nar/gkae974 (2024)

Raney, B.J.* ; Barber, G.P.* ; Benet-Pages, A. ; Casper, J.* ; Clawson, H.* ; Cline, M.S.* ; Diekhans, M.* ; Fischer, C.* ; Navarro Gonzalez, J.* ; Hickey, G.* ; Hinrichs, A.S.* ; Kuhn, R.M.* ; Lee, B.T.* ; Lee, C.M.* ; Le Mercier, P.* ; Miga, K.H.* ; Nassar, L.R.* ; Nejad, P.* ; Paten, B.* ; Perez, G.* ; Schmelter, D.* ; Speir, M.L.* ; Wick, B.D.* ; Zweig, A.S.* ; Haussler, D.* ; Kent, W.J.* ; Haeussler, M.*

The UCSC Genome Browser database: 2024 update.

Nucleic Acids Res. 52, D1082-D1088 (2024)

Stadler, M. ; Lukauskas, S. ; Bartke, T. ; Müller, C.L.

asteRIa enables robust interaction modeling between chromatin modifications and epigenetic readers.

Nucleic Acids Res. 52, 6129-6144 (2024)

Akcan, T.S. ; Vilov, S. ; Heinig, M.

Predictive model of transcriptional elongation control identifies trans regulatory factors from chromatin signatures.

Nucleic Acids Res. 51, 1608-1624 (2023)

Bannister, A.J.* ; Schneider, R. ; Varga-Weisz, P.*

Editorial: Colyn Crane-Robinson (1935-2023).

Nucleic Acids Res. 51, 7709-7713 (2023)

Bredthauer, C. ; Fischer, A.* ; Ahari, A.J.* ; Cao, X.* ; Weber, J.* ; Rad, L.* ; Rad, R.* ; Wachutka, L.* ; Gagneur, J.

Transmicron: Accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens.

Nucleic Acids Res. 51:e21 (2023)

Chanou, A. ; Weiß, M. ; Holler, K. ; Sajid, A. ; Straub, T.* ; Krietsch, J.* ; Sanchi, A.* ; Ummethum, H. ; Lee, C.S.K. ; Kruse, E. ; Trauner, M. ; Werner, M. ; Lalonde, M. ; Lopes, M.* ; Scialdone, A. ; Hamperl, S.

Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency.

Nucleic Acids Res. 51, 12303-12324 (2023)

Keil, P.* ; Wulf, A.* ; Kachariya, N. ; Reuscher, S.* ; Huhn, K.* ; Silbern, I.* ; Altmüller, J.* ; Keller, M.* ; Stehle, R. ; Zarnack, K.* ; Sattler, M. ; Urlaub, H.* ; Sträßer, K.*

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA.

Nucleic Acids Res. 51, 831-851 (2023)

Molitor, L. ; Klostermann, M.* ; Bacher, S. ; Merl-Pham, J. ; Spranger, N. ; Burczyk, S.* ; Ketteler, C. ; Rusha, E. ; Tews, D.* ; Pertek, A. ; Proske, M. ; Busch, A.* ; Reschke, S.* ; Feederle, R. ; Hauck, S.M. ; Blum, H.* ; Drukker, M. ; Fischer-Posovszky, P.* ; König, J.* ; Zarnack, K.* ; Niessing, D.

Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies.

Nucleic Acids Res. 51, 1297-1316 (2023)

Nassar, L.R.* ; Barber, G.P.* ; Benet-Pages, A. ; Casper, J.* ; Clawson, H.* ; Diekhans, M.* ; Fischer, C.* ; Gonzalez, J.N.* ; Hinrichs, A.S.* ; Lee, B.T.* ; Lee, C.M.* ; Muthuraman, P.* ; Nguy, B.* ; Pereira, T.* ; Nejad, P.* ; Perez, G.* ; Raney, B.J.* ; Schmelter, D.* ; Speir, M.L.* ; Wick, B.D.* ; Zweig, A.S.* ; Haussler, D.* ; Kuhn, R.M.* ; Haeussler, M.* ; Kent, W.J.*

The UCSC genome browser database: 2023 update.

Nucleic Acids Res. 51, D1188–D1195 (2023)

Sheikh, A.H.* ; Nawaz, K.* ; Tabassum, N.* ; Almeida-Trapp, M.* ; Mariappan, K.G.* ; Alhoraibi, H.* ; Rayapuram, N.* ; Aranda, M.* ; Groth, M. ; Hirt, H.*

Linker histone H1 modulates defense priming and immunity in plants.

Nucleic Acids Res. 51, 4252-4265 (2023)

Troisi, R.* ; Napolitano, V. ; Rossitto, E.* ; Osman, W.* ; Nagano, M.* ; Wakui, K.* ; Popowicz, G.M. ; Yoshimoto, K.* ; Sica, F.*

Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide.

Nucleic Acids Res. 51, 8880-8890 (2023)

Ugur, E.* ; De La Porte, A. ; Qin, W.* ; Bultmann, S.* ; Ivanova, A.* ; Drukker, M. ; Mann, M.* ; Wierer, M.* ; Leonhardt, H.*

Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components.

Nucleic Acids Res. 51, 2671-2690 (2023)

Witzenberger, M. ; Burczyk, S.* ; Settele, D. ; Mayer, W.* ; Welp, L.M.* ; Heiss, M.* ; Wagner, M.* ; Monecke, T.* ; Janowski, R. ; Carell, T.* ; Urlaub, H.* ; Hauck, S.M. ; Voigt, A.* ; Niessing, D.

Human TRMT2A methylates tRNA and contributes to translation fidelity.

Nucleic Acids Res. 51, 8691-8710 (2023)

Ambike, S. ; Cheng, C.-C. ; Feuerherd, M. ; Velkov, S. ; Baldassi, D.* ; Afridi, S.Q. ; Porras-Gonzalez, D.L. ; Wei, X. ; Hagen, P. ; Kneidinger, N.* ; Stoleriu, M.G.* ; Grass, V. ; Burgstaller, G. ; Pichlmair, A. ; Merkel, O.M. ; Ko, C. ; Michler, T.

Targeting genomic SARS-CoV-2 RNA with siRNAs allows efficient inhibition of viral replication and spread.

Nucleic Acids Res. 50, 333-349 (2022)

Bernaudat, F.* ; Gustems, M. ; Günther, J. ; Oliva, M.F.* ; Buschle, A. ; Göbel,C. ; Pagniez, P.* ; Lupo, J.* ; Signor, L.* ; Müller, C.W.* ; Morand, P.* ; Sattler, M. ; Hammerschmidt, W. ; Petosa, C.*

Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1.

Nucleic Acids Res. 50, 490-511 (2022)

Jones, A. ; Tikhaia, E. ; Mourao, A. ; Sattler, M.

Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1.

Nucleic Acids Res. 50, 2350-2362 (2022)

Shaikh, B.* ; Smith, L.P.* ; Vasilescu, D.* ; Marupilla, G.* ; Wilson, M.* ; Agmon, E.* ; Agnew, H.* ; Andrews, S.S.* ; Anwar, A.* ; Beber, M.E.* ; Bergmann, F.T.* ; Brooks, D.* ; Brusch, L.* ; Calzone, L.* ; Choi, K.* ; Cooper, J.* ; Detloff, J.* ; Drawert, B.* ; Dumontier, M.* ; Ermentrout, G.B.* ; Faeder, J.R.* ; Freiburger, A.P.* ; Fröhlich, F.* ; Funahashi, A.* ; Garny, A.* ; Gennari, J.H.* ; Gleeson, P.* ; Goelzer, A.* ; Haiman, Z.* ; Hasenauer, J.* ; Hellerstein, J.L.* ; Hermjakob, H.* ; Hoops, S.* ; Ison, J.C.* ; Jahn, D.* ; Jakubowski, H.V.* ; Jordan, R.* ; Kalaš, M.* ; König, M.* ; Liebermeister, W.* ; Sheriff, R.S.M.* ; Mandal, S.* ; McDougal, R.* ; Medley, J.K.* ; Mendes, P.* ; Müller, R.* ; Myers, C.J.* ; Naldi, A.* ; Nguyen, T.V.N.* ; Nickerson, D.P.* ; Olivier, B.G.* ; Patoliya, D.* ; Paulevé, L.* ; Petzold, L.R.* ; Priya, A.* ; Rampadarath, A.K.* ; Rohwer, J.M.* ; Saglam, A.S.* ; Singh, D.* ; Sinha, A.* ; Snoep, J.D.* ; Sorby, H.* ; Spangler, R.* ; Starruß, J.* ; Thomas, P.J.* ; van Niekerk, D.* ; Weindl, D. ; Zhang, F.* ; Zhukova, A.* ; Goldberg, A.P.* ; Schaff, J.C.* ; Blinov, M.L.* ; Sauro, H.M.* ; Moraru, I.I.* ; Karr, J.R.*

BioSimulators: A central registry of simulation engines and services for recommending specific tools.

Nucleic Acids Res. 50, W108-W114 (2022)

Stolz, P.* ; Mantero, A.S.* ; Tvardovskiy, A. ; Ugur, E.* ; Wange, L.E.* ; Mulholland, C.B.* ; Cheng, Y.* ; Wierer, M.* ; Enard, W.* ; Schneider, R. ; Bartke, T. ; Leonhardt, H.* ; Elsässer, S.J.* ; Bultmann, S.*

TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation.

Nucleic Acids Res. 50, 8491-8511 (2022)

Tsitsiridis, G. ; Steinkamp, R. ; Giurgiu, M.* ; Brauner, B. ; Fobo, G. ; Frishman, G. ; Montrone, C. ; Ruepp, A.

CORUM: The comprehensive resource of mammalian protein complexes-2022.

Nucleic Acids Res. 51, D539-D545 (2022)

Buschle, A. ; Mrozek-Gorska, P. ; Cernilogar, F.M.* ; Ettinger, A. ; Pich, D. ; Krebs, S.* ; Mocanu, B. ; Blum, H.* ; Schotta, G.* ; Straub, T.* ; Hammerschmidt, W.

Epstein-Barr virus inactivates the transcriptome and disrupts the chromatin architecture of its host cell in the first phase of lytic reactivation.

Nucleic Acids Res. 49, 3217-3241 (2021)

Dieckmann, M.A.* ; Beyvers, S.* ; Nkouamedjo-Fankep, R.C.* ; Hanel, P. ; Jelonek, L.* ; Blom, J.* ; Goesmann, A.*

EDGAR3.0: Comparative genomics and phylogenomics on a scalable infrastructure.

Nucleic Acids Res. 49, W185-W192 (2021)

Manet, E.* ; Polvèche, H.* ; Mure, F.* ; Mrozek-Gorska, P. ; Roisné-Hamelin, F.* ; Hammerschmidt, W. ; Auboeuf, D.* ; Gruffat, H.*

Modulation of alternative splicing during early infection of human primary B lymphocytes with Epstein-Barr virus (EBV): A novel function for the viral EBNA-LP protein.

Nucleic Acids Res. 49, 10657–10676 (2021)

Naarmann-de Vries, I.S.* ; Senatore, R.* ; Moritz, B.* ; Marx, G.* ; Urlaub, H.* ; Niessing, D. ; Ostareck, D.H.* ; Ostareck-Lederer, A.*

Methylated HNRNPK acts on RPS19 to regulate ALOX15 synthesis in erythropoiesis.

Nucleic Acids Res. 49, 3507-3523 (2021)

Petryk, N.* ; Bultmann, S.* ; Bartke, T. ; Defossez, P.-A.*

Staying true to yourself: Mechanisms of DNA methylation maintenance in mammals

Nucleic Acids Res. 49, 3020–3032 (2021)

Zhao, S.* ; Kieser, A.* ; Li, H.Y.* ; Reinking, H.K.* ; Weickert, P.* ; Euteneuer, S.* ; Yaneva, D.* ; Acampora, A.C.* ; Götz, M.J.* ; Feederle, R. ; Stingele, J.*

A ubiquitin switch controls autocatalytic inactivation of the DNA-protein crosslink repair protease SPRTN.

Nucleic Acids Res. 49, 902-915 (2021)

Becker, M. ; Noll-Puchta, H.* ; Amend, D. ; Nolte, F.* ; Fuchs, C. ; Jeremias, I. ; Braun, C.J.*

CLUE: A bioinformatic and wet-lab pipeline for multiplexed cloning of custom sgRNA libraries.

Nucleic Acids Res. 48:e78 (2020)

Binas, O.* ; Tants, J.N.* ; Peter, S.A.* ; Janowski, R. ; Davydova, E.-O. ; Braun, J.* ; Niessing, D. ; Schwalbe, H.* ; Weigand, J.E.* ; Schlundt, A.*

Structural basis for the recognition of transiently structured AU-rich elements by Roquin.

Nucleic Acids Res. 48, 7385-7403 (2020)

Chlis, N.-K. ; Rausch, L.* ; Brocker, T.* ; Kranich, J.* ; Theis, F.J.

Predicting single-cell gene expression profiles of imaging flow cytometry data with machine learning.

Nucleic Acids Res. 48, 11335-11346 (2020)

Escoter Torres, L. ; Greulich, F. ; Quagliarini, F. ; Wierer, M.* ; Uhlenhaut, N.H.

Anti-inflammatory functions of the glucocorticoid receptor require DNA binding.

Nucleic Acids Res. 48, 8393-8407 (2020)

Jung, S. ; von Thülen, T.* ; Yang, I.* ; Laukemper, V.* ; Rupf, B.* ; Janga, H.* ; Panagiotidis, G.-D.* ; Schoen, A.* ; Nicolai, M.* ; Schulte, L.N.* ; Obermann, H.-L.* ; Weber, F.* ; Kaufmann, A.* ; Bauer, S.*

A ribosomal RNA fragment with 2',3'-cyclic phosphate and GTP-binding activity acts as RIG-I ligand.

Nucleic Acids Res. 48, 10397-10412 (2020)

Kochanova, N.Y.* ; Schauer, T.* ; Mathias, G.P.* ; Lukacs, A.* ; Schmidt, A.* ; Flatley, A. ; Schepers, A. ; Thomae, A.W.* ; Imhof, A.*

A multi-layered structure of the interphase chromocenter revealed by proximity-based biotinylation.

Nucleic Acids Res. 48, 4161-4178 (2020)

Monteagudo-Sánchez, A.* ; Hernandez Mora, J.R.* ; Simon, C.* ; Burton, A. ; Tenorio, J.* ; Lapunzina, P.* ; Clark, S.* ; Esteller, M.* ; Kelsey, G.* ; López-Siguero, J.P.* ; de Nanclares, G.P.* ; Torres-Padilla, M.E. ; Monk, D.*

The role of ZFP57 and additional KRAB-zinc finger proteins in the maintenance of human imprinted methylation and multi-locus imprinting disturbances.

Nucleic Acids Res. 48, 11394-11407 (2020)

Bressin, A.* ; Schulte-Sasse, R.* ; Figini, D.* ; Urdaneta, E.C.* ; Beckmann, B.M.* ; Marsico, A.

TriPepSVM: De novo prediction of RNA-binding proteins based on short amino acid motifs.

Nucleic Acids Res. 47, 4406-4417 (2019)

Cernilogar, F.M.* ; Hasenöder ; Wang, Z.* ; Scheibner, K. ; Burtscher, I. ; Sterr, M. ; Smialowski, P. ; Groh, S.* ; Evenroed, I.M.* ; Gilfillan, G.D.* ; Lickert, H. ; Schotta, G.*

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2.

Nucleic Acids Res. 47, 9069-9086 (2019)

Giurgiu, M. ; Reinhard, J. ; Brauner, B. ; Dunger-Kaltenbach, I. ; Fobo, G. ; Frishman, D. ; Montrone, C. ; Ruepp, A.

CORUM: The comprehensive resource of mammalian protein complexes2019.

Nucleic Acids Res. 47, D559-D563 (2019)

Harpprecht, L.* ; Baldi, S.* ; Schauer, T.* ; Schmidt, A.* ; Bange, T.* ; Robles, M.S.* ; Kremmer, E. ; Imhof, A.* ; Becker, P.B.*

A Drosophila cell-free system that senses DNA breaks and triggers phosphorylation signalling.

Nucleic Acids Res. 47, 7444-7459 (2019)

Kubo, M.* ; Nishiyama, T.* ; Tamada, Y.* ; Sano, R.* ; Ishikawa, M.* ; Murata, T.* ; Imai, A.* ; Lang, D.

Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation.

Nucleic Acids Res. 47, 4539-4553 (2019)

Pabis, M. ; Popowicz, G.M. ; Stehle, R. ; Fernández-Ramos, D.* ; Asami, S. ; Warner, L. ; García-Mauriño, S.M.* ; Schlundt, A. ; Martínez-Chantar, M.L.* ; Díaz-Moreno, I.* ; Sattler, M.

HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs.

Nucleic Acids Res. 47, 1011-1029 (2019)

Pabis, M. ; Corsini, L. ; Vincendeau, M. ; Tripsianes, K.* ; Gibson, T.J.* ; Brack-Werner, R. ; Sattler, M.

Modulation of HIV-1 gene expression by binding of a ULM motif in the Rev protein to UHM-containing splicing factors.

Nucleic Acids Res. 47, 4859-4871 (2019)

Rohrmoser, M. ; Kluge, M.* ; Yahia, Y.* ; Gruber-Eber, A. ; Maqbool, M.A.* ; Forné, I.* ; Krebs, S.* ; Blum, H.* ; Greifenberg, A.K.* ; Geyer, M.* ; Descostes, N.* ; Imhof, A.* ; Andrau, J.C.* ; Friedel, C.C.* ; Eick, D.

MIR sequences recruit zinc finger protein ZNF768 to expressed genes.

Nucleic Acids Res. 47, 700-715 (2019)

Tepper, S.* ; Mortusewicz, O.* ; Członka, E.* ; Bello, A.* ; Schmidt, A.* ; Jeschke, J.* ; Fischbach, A.* ; Pfeil, I. ; Petersen-Mahrt, S.K.* ; Mangerich, A.* ; Helleday, T.* ; Leonhardt, H.* ; Jungnickel, B.*

Restriction of AID activity and somatic hypermutation by PARP-1.

Nucleic Acids Res. 47, 7418-7429 (2019)

Angerilli, A.* ; Smialowski, P. ; Rupp, R.A.*

The Xenopus animal cap transcriptome: Building a mucociliary epithelium.

Nucleic Acids Res. 46, 8772-8787 (2018)

Behrens, G.* ; Winzen, R.* ; Rehage, N.* ; Doerrie, A.* ; Barsch, M.* ; Hoffmann, A.L.* ; Hackermueller, J.* ; Tiedje, C.* ; Heissmeyer, V. ; Holtmann, H.*

A translational silencing function of MCPIP1/Regnase-1 specified by the target site context.

Nucleic Acids Res. 46, 4256-4270 (2018)

Fischer, D.S. ; Theis, F.J. ; Yosef, N.*

Impulse model-based differential expression analysis of time course sequencing data.

Nucleic Acids Res. 46:e119 (2018)

Kriegel, F.* ; Matek, C. ; Dršata, T.* ; Kulenkampff, K.* ; Tschirpke, S.* ; Zacharias, M.* ; Lankaš, F.* ; Lipfert, J.*

The temperature dependence of the helical twist of DNA.

Nucleic Acids Res. 46, 7998-8009 (2018)

Lloyd, J.P.B.* ; Lang, D. ; Zimmer, A.D.* ; Causier, B.* ; Reski, R.* ; Davies, B.*

The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens.

Nucleic Acids Res. 46, 5822-5836 (2018)

Alcaraz, N.* ; List, M.* ; Batra, R. ; Vandin, F.* ; Ditzel, H.J.* ; Baumbach, J.*

De novo pathway-based biomarker identification.

Nucleic Acids Res. 45:e151 (2017)

Clauß, K.* ; Popp, A.P.* ; Schulze, L.* ; Hettich, J.* ; Reisser, M.* ; Escoter Torres, L. ; Uhlenhaut, N.H. ; Gebhardt, J.C.M.*

DNA residence time is a regulatory factor of transcription repression.

Nucleic Acids Res. 45, 11121-11130 (2017)

Deng, T.* ; Postnikov, Y.* ; Zhang, S.* ; Garrett, L. ; Becker, L. ; Rácz, I. ; Hölter, S.M. ; Wurst, W. ; Fuchs, H. ; Gailus-Durner, V. ; Hrabě de Angelis, M. ; Bustin, M.*

Interplay between H1 and HMGN epigenetically regulates OLIG1&2 expression and oligodendrocyte differentiation.

Nucleic Acids Res. 45, 3031-3045 (2017)

He, F.* ; Vestergaard, G. ; Peng, W.M.* ; She, Q.* ; Peng, X.*

CRISPR-Cas type I-A Cascade complex couples viral infection surveillance to host transcriptional regulation in the dependence of Csa3b.

Nucleic Acids Res. 45, 1902-1913 (2017)

Kumar, V.* ; Fleming, T.* ; Terjung, S.* ; Gorzelanny, C.* ; Gebhardt, C.* ; Agrawal, R.* ; Mall, M.A.* ; Ranzinger, J.* ; Zeier, M.* ; Madhusudhan, T.* ; Ranjan, S.* ; Isermann, B.* ; Liesz, A.* ; Deshpande, D.* ; Häring, H.-U. ; Biswas, S.K.* ; Reynolds, P.R.* ; Hammes, H.P.* ; Peperkok, R.* ; Angel, P.* ; Herzig, S. ; Nawroth, P.P.

Homeostatic nuclear RAGE-ATM interaction is essential for efficient DNA repair.

Nucleic Acids Res. 45, 10595-10613 (2017)

Lee, H.K. ; Qian, K. ; von Toerne, C. ; Hoerburger, L.* ; Claussnitzer, M. ; Hoffmann, C.* ; Glunk, V. ; Wahl, S. ; Breier, M. ; Eck, F.* ; Jafari, L.* ; Molnos, S. ; Grallert, H. ; Dahlman, I.* ; Arner, P.* ; Brunner, C.* ; Hauner, H. ; Hauck, S.M. ; Laumen, H.

Allele-specific quantitative proteomics unravels molecular mechanisms modulated by cis-regulatory PPARG locus variation.

Nucleic Acids Res. 45, 3266-3279 (2017)

Senís, E.* ; Mockenhaupt, S.* ; Rupp, D.* ; Bauer, T.* ; Paramasivam, N.* ; Knapp, B. ; Gronych, J.* ; Grosse, S.D.* ; Windisch, M.P.* ; Schmidt, F.* ; Theis, F.J. ; Eils, R.* ; Lichter, P.* ; Schlesner, M.* ; Bartenschlager, R.* ; Grimm, D.*

TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus.

Nucleic Acids Res. 45:e3 (2017)

Tants, J.-N. ; Fesser, S.* ; Kern, T. ; Stehle, R. ; Geerlof, A. ; Wunderlich, C.* ; Juen, M.* ; Hartlmüller, C. ; Böttcher, R.* ; Kunzelmann, S.* ; Lange, O.L.* ; Kreutz, C.* ; Förstemann, K.* ; Sattler, M.

Molecular basis for asymmetry sensing of siRNAs by the Drosophila Loqs-PD/Dcr-2 complex in RNA interference.

Nucleic Acids Res. 45, 12536-12550 (2017)

Zhang, D.* ; Wu, B.L.* ; Wang, P.* ; Wang, Y.* ; Lu, P.* ; Nechiporuk, T.* ; Floß, T. ; Greally, J.M.* ; Zheng, D.* ; Zhou, B.*

Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts.

Nucleic Acids Res. 45, 3102-3115 (2017)

Gunnell, A.* ; Webb, H.M.* ; Wood, C.D.* ; McClellan, M.J.* ; Wichaidit, B.* ; Kempkes, B. ; Jenner, R.G.* ; Osborne, C.* ; Farrell, P.J.* ; West, M.J.*

RUNX super-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth.

Nucleic Acids Res. 44, 4636-4650 (2016)

Haar, J.* ; Contrant, M.* ; Bernhardt, K.* ; Feederle, R. ; Diederichs, S.* ; Pfeffer, S.* ; Delecluse, H.J.*

The expression of a viral microRNA is regulated by clustering to allow optimal B cell transformation.

Nucleic Acids Res. 44, 1326-1341 (2016)

Huerta-Cepas, J.* ; Szklarczyk, D.* ; Forslund, K.* ; Cook, H.* ; Heller, D.* ; Walter, M.C. ; Rattei, T.* ; Mende, D.R.* ; Sunagawa, S.* ; Kuhn, M.* ; Jensen, L.J.* ; von Mering, C.* ; Bork, P.*

eggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

Nucleic Acids Res. 44, D286-D293 (2016)

Ketterer, S.* ; Gladis, L.* ; Kozica, A.* ; Meier, M.

Engineering and characterization of fluorogenic glycine riboswitches.

Nucleic Acids Res. 44, 5983-5992 (2016)

Nagarajan, S.* ; Bedi, U.* ; Budida, A.* ; Hamdan, F.H.* ; Mishra, V.K.* ; Najafova, Z.* ; Xie, W.* ; Alawi, M.* ; Indenbirken, D.* ; Knapp, S.* ; Chiang, C.M.* ; Grundhoff, A.* ; Kari, V.* ; Scheel, C. ; Wegwitz, F.* ; Johnsen, S.A.*

BRD4 promotes p63 and GRHL3 expression downstream of FOXO in mammary epithelial cells.

Nucleic Acids Res. 45, 3130-3145 (2016)

Spannagl, M. ; Nussbaumer, T. ; Bader, K.C. ; Martis, M.M. ; Seidel, M. ; Kugler, K.G. ; Gundlach, H. ; Mayer, K.F.X.

PGSB PlantsDB: Updates to the database framework for comparative plant genome research.

Nucleic Acids Res. 44, D1141-D1147 (2016)

Anosova, I. ; Melnik, S.* ; Tripsianes, K. ; Kateb, F. ; Grummt, I.* ; Sattler, M.

A novel RNA binding surface of the TAM domain of TIP5/BAZ2A mediates epigenetic regulation of rRNA genes.

Nucleic Acids Res. 43, 5208-5220 (2015)

Cheng, Y. ; Perocchi, F.

ProtPhylo: Identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling.

Nucleic Acids Res. 41, W160-W168 (2015)

INFRAFRONTIER Consortium (de Castro, A. ; Fessele, S. ; Steinkamp, R. ; Hagn, M. ; Raess, M. ; Hrabě de Angelis, M. ; Meehan, T.F.*)

INFRAFRONTIER - providing mutant mouse resources as research tools for the international scientific community.

Nucleic Acids Res. 53, D1171-D1175 (2015)

Ketterer, S.* ; Fuchs, D.* ; Weber, W.* ; Meier, M.

Systematic reconstruction of binding and stability landscapes of the fluorogenic aptamer spinach.

Nucleic Acids Res. 43, 9564-9572 (2015)

Mannil, D. ; Vogt, I. ; Prinz, J. ; Campillos, M.

Organ system heterogeneity DB: A database for the visualization of phenotypes at the organ system level.

Nucleic Acids Res. 43, D900-D906 (2015)

Mulholland, C.B.* ; Smets, M.* ; Schmidtmann, E.* ; Leidescher, S.* ; Markaki, Y.* ; Hofweber, M.* ; Qin, W.* ; Manzo, M.* ; Kremmer, E. ; Thanisch, K.* ; Bauer, C.* ; Rombaut, P.* ; Herzog, F.* ; Leonhardt, H.* ; Bultmann, S.*

A modular open platform for systematic functional studies under physiological conditions.

Nucleic Acids Res. 43:e112 (2015)

Schraivogel, D.* ; Schindler, S.G.* ; Danner, J.* ; Kremmer, E. ; Pfaff, J.* ; Hannus, S.* ; Depping, R.* ; Meister, G.*

Importin-β facilitates nuclear import of human GW proteins and balances cytoplasmic gene silencing protein levels.

Nucleic Acids Res. 43, 7447-7461 (2015)

Truong, D.J.J. ; Kühner, K. ; Kühn, R. ; Werfel, S.* ; Engelhardt, S.* ; Wurst, W. ; Ortiz, O.

Development of an intein-mediated split-Cas9 system for gene therapy.

Nucleic Acids Res. 43, 6450-6458 (2015)

Arnold, R.* ; Goldenberg, F.* ; Mewes, H.-W. ; Rattei, T.*

SIMAP - the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.

Nucleic Acids Res. 42, D279-D284 (2014)

Bazot, Q.* ; Deschamps, T.* ; Tafforeau, L.* ; Siouda, M.* ; Leblanc, P.* ; Harth-Hertle, M.L. ; Rabourdin-Combe, C.* ; Lotteau, V.* ; Kempkes, B. ; Tommasino, M.* ; Gruffat, H.* ; Manet, E.*

Epstein-Barr virus nuclear antigen 3A protein regulates CDKN2B transcription via interaction with MIZ-1.

Nucleic Acids Res. 42, 9700-9716 (2014)

Bleves, S.* ; Dunger, I. ; Walter, M.C. ; Frangoulidis, D.* ; Kastenmüller, G. ; Voulhoux, R.* ; Ruepp, A.

HoPaCI-DB: Host-Pseudomonas and Coxiella interaction database.

Nucleic Acids Res. 42, D671-D676 (2014)

Blohm, P. ; Frishman, G. ; Smialowski, P. ; Goebels, F.* ; Wachinger, B. ; Ruepp, A. ; Frishman, D.

Negatome 2.0: A database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis.

Nucleic Acids Res. 42, D396-D400 (2014)

Ellwanger, D.C. ; Leonhardt, J. ; Mewes, H.-W.

Large-scale modeling of condition-specific gene regulatory networks by information integration and inference.

Nucleic Acids Res. 42:e166 (2014)

Frankenberger, S. ; Davari, K.* ; Fischer-Burkart, S. ; Böttcher, K.* ; Tomi, N.S.* ; Zimber-Strobl, U. ; Jungnickel, B.

Checkpoint kinase 1 negatively regulates somatic hypermutation.

Nucleic Acids Res. 42, 3666-3674 (2014)

Gustems, M. ; Woellmer, A. ; Rothbauer, U.* ; Eck, S.H. ; Wieland, T. ; Lutter, D. ; Hammerschmidt, W.

c-Jun/c-Fos heterodimers regulate cellular genes via a newly identified class of methylated DNA sequence motifs.

Nucleic Acids Res. 42, 3059-3072 (2014)

Heim, A.* ; Grimm, C.* ; Müller, U.* ; Häußler, S.* ; Mackeen, M.M.* ; Merl, J. ; Hauck, S.M. ; Kessler, B.M.* ; Schofield, C.J.* ; Wolf, A. ; Böttger, A.*

Jumonji domain containing protein 6 (Jmjd6) modulates splicing and specifically interacts with arginine-serine-rich (RS) domains of SR- and SR-like proteins.

Nucleic Acids Res. 42, 7833-7850 (2014)

Ullius, A.* ; Luscher-Firzlaff, J.* ; Costa, I.G.* ; Walsemann, G.* ; Forst, A.H.* ; Gusmao, E.G.* ; Kapelle, K. ; Kleine, H.* ; Kremmer, E. ; Vervoorts, J.* ; Lüscher, B.*

The interaction of MYC with the trithorax protein ASH2L promotes gene transcription by regulating H3K27 modification.

Nucleic Acids Res. 42, 6901-6920 (2014)

Wang, I. ; Hennig, J. ; Jagtap, P.K. ; Sonntag, M. ; Valcárcel, J.* ; Sattler, M.

Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1.

Nucleic Acids Res. 42, 5949-5966 (2014)

Chursov, A.* ; Kopetzky, S.J.* ; Bocharov, G.* ; Frishman, D. ; Shneider, A.*

RNAtips: Analysis of temperature-induced changes of RNA secondary structure.

Nucleic Acids Res. 41, W486-W491 (2013)

Chursov, A.* ; Frishman, D. ; Shneider, A.*

Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution.

Nucleic Acids Res. 41, 7854-7860 (2013)

de la Vega, L.* ; Hornung, J.* ; Kremmer, E. ; Milanovic, M.* ; Schmitz, M.L.*

Homeodomain-interacting protein kinase 2-dependent repression of myogenic differentiation is relieved by its caspase-mediated cleavage.

Nucleic Acids Res. 41, 5731-5745 (2013)

Garg, D. ; Beribisky, A.V. ; Ponterini, G.* ; Ligabue, A.* ; Marverti, G.* ; Martello, A.* ; Costi, M.P.* ; Sattler, M. ; Wade, R.C.*

Translational repression of thymidylate synthase by targeting its mRNA.

Nucleic Acids Res. 41, 4159-4170 (2013)

Gu, B.* ; Eick, D. ; Bensaude, O.*

CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo.

Nucleic Acids Res. 41, 1591-1603 (2013)

Ivankov, D.N.* ; Bogatyreva, N.S.* ; Honigschmid, P.* ; Dislich, B.* ; Högl, S.* ; Kuhn, P.H.* ; Frishman, D. ; Lichtenthaler, S.F.*

QARIP: A web server for quantitative proteomic analysis of regulated intramembrane proteolysis.

Nucleic Acids Res. 41, W459-W464 (2013)

Nussbaumer, T. ; Martis, M.M. ; Roessner, S.K. ; Pfeifer, M. ; Bader, K.C. ; Sharma, S. ; Gundlach, H. ; Spannagl, M.

MIPS PlantsDB: A database framework for comparative plant genome research.

Nucleic Acids Res. 41, D1144-D1151 (2013)

Sass, S. ; Buettner, F. ; Müller, N.S. ; Theis, F.J.

A modular framework for gene set analysis integrating multilevel omics data.

Nucleic Acids Res. 41, 9622-9633 (2013)

Schneider, K.* ; Fuchs, C. ; Dobay, A.* ; Rottach, A.* ; Qin, W.H.* ; Wolf, P.* ; Alvarez-Castro, J.M.* ; Nalaskowski, M.M.* ; Kremmer, E. ; Schmid, V.* ; Leonhardt, H.* ; Schermelleh, L.*

Dissection of cell cycle-dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling.

Nucleic Acids Res. 41, 4860-4876 (2013)

Zhang, Y.-Y. ; Madl, T. ; Bagdiul, I.* ; Kern, T. ; Kang, H.-S. ; Zou, P. ; Mäusbacher, N.* ; Sieber, S.A.* ; Krämer, A.* ; Sattler, M.

Structure, phosphorylation and U2AF65 binding of the N-terminal domain of splicing factor 1 during 3'-splice site recognition.

Nucleic Acids Res. 41, 1343-1354 (2013)

Arakawa, H. ; Bednar, T.* ; Wang, M.* ; Paul, K.* ; Mladenov, E.* ; Bencsik-Theilen, A.A.* ; Iliakis, G.*

Functional redundancy between DNA ligases I and III in DNA replication in vertebrate cells.

Nucleic Acids Res. 40, 2599-2610 (2012)

Bönisch, C.* ; Schneider, K.* ; Pünzeler, S.* ; Wiedemann, S.M.* ; Bielmeier, C.* ; Bocola, M.* ; Eberl, H.C.* ; Kuegel, W.* ; Neumann, J.* ; Kremmer, E. ; Leonhardt, H.* ; Mann, M.* ; Michaelis, J.* ; Schermelleh, L.* ; Hake, S.B.*

H2A.Z.2.2 is an alternatively spliced histone H2A.Z variant that causes severe nucleosome destabilization.

Nucleic Acids Res. 40, 5951-5964 (2012)

Chursov, A.* ; Walter, M.C. ; Schmidt, T. ; Mironov, A.* ; Shneider, A.* ; Frishman, D.

Sequence-structure relationships in yeast mRNAs.

Nucleic Acids Res. 40, 956-962 (2012)

He, Y.* ; Zhang, M.* ; Ju, Y.* ; Yu, Z.* ; Lv, D.* ; Sun, H.* ; Yuan, W.* ; He, F.* ; Zhang, J.* ; Li, H.* ; Li, J.* ; Wang-Sattler, R. ; Li, Y.* ; Zhang, G.* ; Xie, L.*

dbDEPC 2.0: Updated database of differentially expressed proteins in human cancers.

Nucleic Acids Res. 40, D964-D971 (2012)

Villar-Garea, A.* ; Forne, I.* ; Vetter, I.* ; Kremmer, E. ; Thomae, A.* ; Imhof, A.*

Developmental regulation of N-terminal H2B methylation in Drosophila melanogaster.

Nucleic Acids Res. 40, 1536-1549 (2012)

Antonov, A.V.

BioProfiling.de: Analytical web portal for high-throughput cell biology.

Nucleic Acids Res. 39, W323-W327 (2011)

Felle, M.* ; Joppien, S.* ; Németh, A.* ; Diermeier, S.* ; Thalhammer, V.* ; Dobner, T.* ; Kremmer, E. ; Kappler, R.* ; Längst, G.

The USP7/Dnmt1 complex stimulates the DNA methylation activity of Dnmt1 and regulates the stability of UHRF1.

Nucleic Acids Res. 39, 8355-8365 (2011)

Jehl, M.A.* ; Arnold, R.* ; Rattei, T.*

Effective--a database of predicted secreted bacterial proteins.

Nucleic Acids Res. 39, D591-D595 (2011)

Kantlehner, M.* ; Kirchner, R.* ; Hartmann, P.* ; Ellwart, J.W. ; Alunni-Fabbroni, M.* ; Schumacher, A.*

A high-throughput DNA methylation analysis of a single cell.

Nucleic Acids Res. 39, e44:e44 (2011)

Luo, Q.* ; Pagel, P. ; Vilne, B.* ; Frishman, D.

DIMA 3.0: Domain Interaction Map.

Nucleic Acids Res. 39, 1, D724-D729 (2011)

Ringwald, M.* ; Iyer, V.* ; Mason, J.C.* ; Stone, K.R.* ; Tadepally, H.D.* ; Kadin, J.A.* ; Bult, C.J.* ; Eppig, J.T.* ; Oakley, D.J.* ; Briois, S.* ; Stupka, E.* ; Maselli, V.* ; Smedley, D.* ; Liu, S.Y.* ; Hansen, J. ; Baldock, R.* ; Hicks, G.G.* ; Skarnes, W.C.*

The IKMC web portal: A central point of entry to data and resources from the International Knockout Mouse Consortium.

Nucleic Acids Res. 39, 1, D849-D855 (2011)

Wong, P. ; Walter, M. ; Lee, W. ; Mannhaupt, G. ; Münsterkötter, M. ; Mewes, H.-W. ; Adam, G.* ; Güldener, U.

FGDB: Revisiting the genome annotation of the plant pathogen Fusarium graminearum.

Nucleic Acids Res. 39, D637-D639 (2011)

Antonov, A.V. ; Schmidt, E.E.* ; Dietmann, S. ; Krestyaninova, M.* ; Hermjakob, H.*

R spider: A network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.

Nucleic Acids Res. 38, 2, W78-W83 (2010)

Dietmann, S.* ; Lee, W. ; Wong, P. ; Rodchenkov, I.* ; Antonov, A.V.

CCancer: A bird's eye view on gene lists reported in cancer-related studies.

Nucleic Acids Res. 38, 2, W118-W123 (2010)

Ertongur, I. ; Tomi, N.S. ; Kutzera, A. ; Fischer-Burkart, S. ; Jungnickel, B.

Ubc13 dosage is critical for immunoglobulin gene conversion and gene targeting in vertebrate cells.

Nucleic Acids Res. 38, 4701-4707 (2010)

Mewes, H.-W. ; Ruepp, A. ; Theis, F.J. ; Rattei, T.* ; Walter, M.C. ; Frishman, D. ; Suhre, K. ; Spannagl, M. ; Mayer, K.F.X. ; Stuempflen, V. ; Antonov, A.

MIPS: Curated databases and comprehensive secondary data resources in 2010.

Nucleic Acids Res. 39, 1, D220-D224 (2010)

Morgan, H.* ; Beck, T.* ; Blake, A.* ; Gates, H.* ; Adams, N.* ; Debouzy, G.* ; Leblanc, S.* ; Lengger, C. ; Maier, H. ; Melvin, D.* ; Meziane, H.* ; Richardson, D.* ; Wells, S.* ; White, J.* ; Wood, J.* ; EUMODIC Consortium (Hrabě de Angelis, M. ; Gailus-Durner, V. ; Fuchs, H. ; Adler, T. ; Aguilar-Pimentel, J.A. ; Becker, L. ; Beckeredjian, R ; Busch, D.H. ; Calzada-Wack, J. ; Da Silva-Buttkus, P. ; Esposito, I. ; Favor, J. ; Fleischmann, W. ; Garrett, L. ; Glasl, L. ; Götz, A. ; Graw, J. ; Hans, W, ; Hölter, S.M. ; Ivandic, B. ; Katus, H.A. ; Klingenspor, M. ; Klopstock, T. ; Lengger, C. ; Ludwig, T. ; Maier, H. ; Micklich, K. ; Minxuan, S. ; Naton, B. ; Neff, F. ; Ollert, M. ; Puk, O. ; Quintanilla-Fend, L. ; Rácz, I. ; Rathkolb, B. ; Rozman, J. ; Schäble, K.-H. ; Schiller, E. ; Schrewe, A. ; Steinkamp, R. ; Stoeger, C. ; Stöger, T. ; Schulz, S. ; Tost, M. ; Treise, I. ; Vogt Weisenhorn, D.M. ; Willershäuser, M. ; Wolf, E. ; Zimprich, A. ; Wurst, W. ; Zeh, R.M. ; Zimmer, A.) ; Hrabě de Angelis, M. ; Brown, S.* ; Hancock, J.M.* ; Mallon, A.M.*

EuroPhenome: A repository for high-throughput mouse phenotyping data.

Nucleic Acids Res. 38, 1, D577-D585 (2010)

Rattei, T.* ; Tischler, P.* ; Götz, S.* ; Jehl, M.A.* ; Hoser, J.D.S.* ; Arnold, R.* ; Conesa, A.* ; Mewes, H.-W.

SIMAP - a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.

Nucleic Acids Res. 38, 1, D223-D226 (2010)

Ruepp, A. ; Wägele, B. ; Lechner, M. ; Brauner, B. ; Dunger-Kaltenbach, I. ; Fobo, G. ; Frishman, G. ; Montrone, C. ; Mewes, H.-W.

CORUM: The comprehensive resource of mammalian protein complexes - 2009.

Nucleic Acids Res. 38, 1, D497-D501 (2010)

Schebelle, L. ; Wolf, C. ; Stribl, C.B. ; Javaheri, T. ; Schnütgen, F.* ; Ettinger, A. ; Ivics, Z.* ; Hansen, J. ; Ruiz, P.* ; von Melchner, H.* ; Wurst, W. ; Floß, T.

Efficient conditional and promoter-specific in vivo expression of cDNAs of choice by taking advantage of recombinase-mediated cassette exchange using FlEx gene traps.

Nucleic Acids Res. 38, e106-e106:e106 (2010)

Smialowski, P. ; Pagel, P. ; Wong, P. ; Brauner, B. ; Dunger, I. ; Fobo, G. ; Frishman, G. ; Montrone, C. ; Rattei, T.* ; Frishman, D. ; Ruepp, A.

The Negatome database: A reference set of non-interacting protein pairs.

Nucleic Acids Res. 38, 1, D540-D544 (2010)

Steininger, S. ; Ahne, F. ; Winkler, K. ; Kleinschmidt, A. ; Eckardt-Schupp, F. ; Mörtl, S.

A novel function for the Mre11-Rad50-Xrs2 complex in base excision repair.

Nucleic Acids Res. 38, 1853-1865 (2010)

Wilkinson, P.* ; Sengerova, J.* ; Matteoni, R.* ; Chen, C-K.* ; Soulat, G.* ; Ureta-Vidal, A.* ; Fessele, S. ; Hagn, M. ; Massimi, M.* ; Pickford, K.* ; Butler, R.H.* ; Marschall, S. ; Mallon, A.-M.* ; Pickard, A.* ; Raspa, M.* ; Scavizzi, F.* ; Fray, M.* ; Larrigaldie, V.* ; Leyritz, J.* ; Birney, E.* ; Tocchini-Valentini, G.P.* ; Brown, S.* ; Herault, Y.* ; Montoliu, L.* ; Hrabě de Angelis, M. ; Smedley, D.*

EMMA - mouse mutant resources for the international scientific community.

Nucleic Acids Res. 38, D570-D576 (2010)

Antonov, A.V. ; Dietmann, S. ; Wong, P. ; Lutter, D. ; Mewes, H.-W.

GeneSet2miRNA: Finding the signature of cooperative miRNA activities in the gene lists.

Nucleic Acids Res. 37, Suppl. S, W323-W328 (2009)

Hackenberg, M.* ; Sturm, M. ; Langenberger, D.* ; Falcón-Pérez, J.M.* ; Aransay, A.M.*

miRanalyzer: A microRNA detection and analysis tool for next-generation sequencing experiments.

Nucleic Acids Res. 37, (Suppl.1), W68-W76 (2009)

Stephan, H.* ; Concannon, C.* ; Kremmer, E. ; Carty, M.P.* ; Nasheuer, H.P.*

Ionizing radiation-dependent and independent phosphorylation of the 32-kDa subunit of replication protein A during mitosis.

Nucleic Acids Res. 37, 6028-6041 (2009)

Antonov, A.V. ; Schmidt, T.* ; Wang, Y. ; Mewes, H.-W.

ProfCom: A web tool for profiling the complex functionality of gene groups identified from high-throughput data.

Nucleic Acids Res. 36, W347-W351 (2008)

Arakawa, H. ; Kudo, H. ; Batrak, V. ; Caldwell, R.B. ; Rieger, M. ; Ellwart, J.W. ; Buerstedde, J.-M.

Protein evolution by hypermutation and selection in the B cell line DT40.

Nucleic Acids Res. 36:e1 (2008)

Barth, S.* ; Pfuhl, T.* ; Mamiani, A.* ; Ehses, C.* ; Roemer, K.* ; Kremmer, E. ; Jäker, C.* ; Höck, J.* ; Meister, G.* ; Grässer, F.A.*

Epstein-Barr virus-encoded microRNA miR-BART2 down-regulates the viral DNA polymerase BALF5.

Nucleic Acids Res. 36, 666-675 (2008)

Duszczyk, M.M. ; Zanier, K.* ; Sattler, M.

A NMR strategy to unambiguously distinguish nucleic acid hairpin and duplex conformations applied to a Xist RNA A-repeat.

Nucleic Acids Res. 36, 7068-7077 (2008)

Greiner, S.* ; Wang, X. ; Rauwolf, U.* ; Silber, M.V.* ; Mayer, K.F.X. ; Meurer, J.* ; Haberer, G. ; Herrmann, R.G.*

The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. Sequence evaluation and plastome evolution.

Nucleic Acids Res. 36, 2366-2378 (2008)

Izzo, A.* ; Regnard, C.* ; Morales, V.* ; Kremmer, E. ; Becker, P.B.*

Structure-function analysis of the RNA helicase maleless.

Nucleic Acids Res. 36, 950-962 (2008)

Mewes, H.-W. ; Dietmann, S. ; Frishman, D.* ; Gregory, R. ; Mannhaupt, G. ; Mayer, K.F.X. ; Münsterkötter, M. ; Ruepp, A. ; Spannagl, M. ; Stuempflen, V. ; Rattei, T.*

MIPS: Analysis and annotation of genome information in 2007.

Nucleic Acids Res. 36, D196-D201 (2008)

Mierau, M. ; Drexler, G.A. ; Kutzera, A. ; Braunschmidt, K. ; Ellwart, J.W. ; Eckardt-Schupp, F. ; Fritz, E.* ; Bachl, J.* ; Jungnickel, B.

Non-conservative homologous recombination in human B lymphocytes is promoted by activation-induced cytidine deaminase and transcription.

Nucleic Acids Res. 36, 5591-5601 (2008)

Pagel, P. ; Oesterheld, M. ; Tovstukhina, O.* ; Strack, N.* ; Stuempflen, V. ; Frishman, D.

DIMA 2.0 - predicted and known domain interactions.

Nucleic Acids Res. 36, D651-655 (2008)

Pich, D. ; Hummer, S. ; Spindler, M.-P. ; Schepers, A. ; Hammerschmidt, W.

Conditional gene vectors regulated in cis.

Nucleic Acids Res. 36:e83 (2008)

Rattei, T.* ; Tischler, P.* ; Arnold, R.* ; Hamberger, F.* ; Krebs, J.* ; Krumsiek, J.* ; Wachinger, B.* ; Stuempflen, V. ; Mewes, H.-W.

SIMAP-structuring the network of protein similarities.

Nucleic Acids Res. 36, D289-D292 (2008)

Ruepp, A. ; Brauner, B. ; Dunger-Kaltenbach, I. ; Frishman, G. ; Montrone, C. ; Stransky, M. ; Wägele, B. ; Schmidt, T.* ; Doudieu, O.N. ; Stuempflen, V. ; Mewes, H.-W.

CORUM: The comprehensive resource of mammalian protein complexes.

Nucleic Acids Res. 36, D646-D650 (2008)

Schnütgen, F.* ; Hansen, J. ; De-Zolt, S.* ; Horn, C.* ; Lutz, M.* ; Floß, T. ; Wurst, W. ; Ruiz Noppinger, P.* ; von Melchner, H.*

Enhanced gene trapping in mouse embryonic stem cells.

Nucleic Acids Res. 36:e133 (2008)

Suhre, K. ; Schmitt-Kopplin, P.

MassTRIX: Mass translator into pathways.

Nucleic Acids Res. 36, W481-W484 (2008)

Tanaka, T.* ; Antonio, B.A.* ; Kikuchi, S.* ; Matsumoto, T.* ; Nagamura, Y.* ; Numa, H.* ; Sakai, H.* ; Wu, J.* ; Itoh, T.* ; Sasaki, T.* ; Aono, R.* ; Fujii, Y.* ; Habara, T.* ; Harada, E.* ; Kanno, M.* ; Kawahara, Y.* ; Kawashima, H.* ; Kubooka, H.* ; Matsuya, A.* ; Nakaoka, H.* ; Saichi, N.* ; Sanbonmatsu, R.* ; Sato, Y.* ; Shinso, Y.* ; Suzuki, M.* ; Takeda, J.* ; Tanino, M.* ; Todokoro, F.* ; Yamaguchi, K.* ; Yamamoto, N.* ; Yamasaki, C.* ; Imanishi, T.* ; Okido, T.* ; Tada, M.* ; Ikeo, K.* ; Tateno, Y.* ; Gojobori, T.* ; Lin, YC.* ; Wei, F.J.* ; Hsing, Y.I.* ; Zhao, Q.* ; Han, B.* ; Kramer, M.R.* ; McCombie, R.W.* ; Lonsdale, D.* ; O'Donovan, C.C.* ; Whitfield, E.J.* ; Apweiler, R.* ; Koyanagi, K.O.* ; Khurana, J.P.* ; Raghuvanshi, S.* ; Singh, N.K.* ; Tyagi, A.K.* ; Haberer, G. ; Fujisawa, M.* ; Hosokawa, S.* ; Ito, Y.* ; Ikawa, H.* ; Shibata, M.* ; Yamamoto, M.* ; Bruskiewich, R.M.* ; Hoen, D.R.* ; Bureau, T.E.* ; Namiki, N.* ; Ohyanagi, H.* ; Sakai, Y.* ; Nobushima, S.* ; Sakata, K.* ; Barrero, R.A.* ; Souvorov, A.* ; Smith-White, B.* ; Tatusova, T.* ; An, S.* ; An, G.* ; Oota, S.* ; Fuks, G.* ; Messing, J.* ; Christie, K.R.* ; Lieberherr, D.* ; Kim, H.* ; Zuccolo, A.* ; Wing, R.A.* ; Nobuta, K.* ; Green, P.J.* ; Lu, C.* ; Meyers, B.C.* ; Chaparro, C.* ; Piegu, B.* ; Panaud, O.* ; Echeverria, M.* ; Rice Annotation Project (*)

The Rice Annotation Project Database (RAP-DB): 2008 update.

Nucleic Acids Res. 36, D1028-D1033 (2008)

Wägele, B. ; Schmidt, T.* ; Mewes, H.-W. ; Ruepp, A.

OREST: The online resource for EST analysis.

Nucleic Acids Res. 36, W140-W144 (2008)

Walter, M.C. ; Rattei, T.* ; Arnold, R.* ; Güldener, U. ; Münsterkötter, M. ; Nenova, K. ; Kastenmüller, G. ; Tischler, P.* ; Wölling, A.* ; Volz, A.* ; Pongratz, N.* ; Jost, R.* ; Mewes, H.-W. ; Frishman, D.

Pedant covers all complete RefSeq genomes.

Nucleic Acids Res. 37, D408-D411 (2008)

Fiegler, H.* ; Geigl, J.B.* ; Langer, S.* ; Rigler, D.* ; Porter, K.* ; Unger, K. ; Carter, N.P.* ; Speicher, M.R.*

High resolution array-CGH analysis of single cells.

Nucleic Acids Res. 35:e15 (2007)

Hitz, C. ; Wurst, W. ; Kühn, R.

Conditional brain-specific knockdown of MAPK using Cre/loxP regulated RNA interference.

Nucleic Acids Res. 35:e90 (2007)

Hölzel, M. ; Rohrmoser, M. ; Orban, M. ; Hömig, C. ; Harasim, T. ; Malamoussi, A. ; Gruber-Eber, A. ; Heissmeyer, V. ; Bornkamm, G.W. ; Eick, D.

Rapid conditional knock-down–knock-in system for mammalian cells.

Nucleic Acids Res. 35:e17 (2007)

Hölzel, M. ; Grimm, T. ; Rohrmoser, M. ; Malamoussi, A. ; Harasim, T. ; Gruber-Eber, A. ; Kremmer, E. ; Eick, D.

The BRCT domain of mammalian Pes1 is crucial for nucleolar localization and rRNA processing.

Nucleic Acids Res. 35, 789-800 (2007)

Messaoudi, L.* ; Yang, Y.G.* ; Kinomura, A.* ; Stavreva, D.A.* ; Yan, G.* ; Bortolin-Cavaillé, ML.* ; Arakawa, H. ; Buerstedde, J.M. ; Hainaut, P.* ; Cavaillé, J.* ; Takata, M.* ; van Dyck, E.*

Subcellular distribution of human RDM1 protein isoforms and their nucleolar accumulation in response to heat shock and proteotoxic stress.

Nucleic Acids Res. 35, 6571-6587 (2007)

Riley, M.L. ; Schmidt, T.* ; Artamonova, I.I. ; Wagner, C.* ; Volz, A.* ; Heumann, K.* ; Mewes, H.-W. ; Frishman, D.

PEDANT genome database: 10 years online.

Nucleic Acids Res. 35, D354-D357 (2007)

Spannagl, M. ; Noubibou, O. ; Haase, D. ; Yang, L. ; Gundlach, H. ; Hindemitt, T. ; Klee, K. ; Haberer, G. ; Schoof, H. ; Mayer, K.F.X.

MIPSPlantsDB - plant database resource for integrative and comparative plant genome research.

Nucleic Acids Res. 35, 834-840 (2007)

Antonov, A.V. ; Tetko, I.V. ; Mewes, H.-W.

A systematic approach to infer biological relevance and biases of gene network structures.

Nucleic Acids Res. 34, e6:E6 (2006)

De-Zolt, S.* ; Schnütgen, F.* ; Seisenberger, C. ; Hansen, J. ; Hollatz, M. ; Floß, T. ; Ruiz, P.* ; Wurst, W. ; von Melchner, H.*

High-throughput trapping of secretory pathway genes in mouse embryonic stem cells.

Nucleic Acids Res. 34:e25 (2006)

Grimm, T. ; Hölzel, M. ; Rohrmoser, M. ; Harasim, T. ; Malamoussi, A. ; Gruber-Eber, A. ; Kremmer, E. ; Eick, D.

Dominant-negative Pes1 mutants inhibit ribosomal RNA processing and cell proliferation via incorporation into the PeBoW-complex.

Nucleic Acids Res. 34, 3030-3043 (2006)

Güldener, U. ; Münsterkötter, M. ; Oesterheld, M. ; Pagel, P. ; Ruepp, A. ; Mewes, H.-W. ; Stuempflen, V.

MPact: The MIPS protein interaction resource on yeast.

Nucleic Acids Res. 34, 436-441 (2006)

Güldener, U. ; Mannhaupt, G.* ; Münsterkötter, M. ; Haase, M. ; Oesterheld, M. ; Stuempflen, V. ; Mewes, H.-W. ; Adam, G.*

FGDB: A comprehensive fungal genome resource on the plant pathogen Fusarium graminearum.

Nucleic Acids Res. 34, D456-D458 (2006)

Mewes, H.-W. ; Frishman, D.* ; Mayer, K.F.X. ; Münsterkötter, M. ; Noubibou, O. ; Pagel, P. ; Rattei, T.* ; Oesterheld, M. ; Ruepp, A. ; Stuempflen, V.

MIPS: Analysis and annotation of proteins from whole genomes in 2005.

Nucleic Acids Res. 34, D169-D172 (2006)

Nord, A.S.* ; Chang, P.J.* ; Conklin, B.R.* ; Cox, A.V.* ; Harper, C.A.* ; Hicks, G.G.* ; Huang, C.C.* ; Johns, S.J.* ; Kawamoto, M.* ; Liu, S.* ; Meng, E.C.* ; Morris, J.H.* ; Rossant, J.* ; Ruiz, P.* ; Skarnes, W.C.* ; Soriano, P.* ; Stanford, W.L.* ; Stryke, D.* ; von, Melchner, H.* ; Wurst, W. ; Yamamura, K.* ; Young, S.G.* ; Babbitt, P.C.* ; Ferrin, T.E.

The International Gene Trap Consortium website: A portal to all publicly available gene trap cell lines in mouse.

Nucleic Acids Res. 34, D642-D648 (2006)

Prokisch, H. ; Andreoli, C.* ; Ahting, U.* ; Heiss, K.* ; Ruepp, A. ; Scharfe, C.* ; Meitinger, T.

MitoP2: The mitochondrial proteome database-now including mouse data.

Nucleic Acids Res. 34, D705-D711 (2006)

Rattei, T.* ; Arnold, R. ; Tischler, P. ; Lindner, D.* ; Stuempflen, V. ; Mewes, H.-W.

Nucleic Acids Res. 34, 252-256 (2006)

Ruepp, A. ; Doudieu, O.N. ; van den Oever, J. ; Brauner, B. ; Dunger-Kaltenbach, I. ; Fobo, G. ; Frishman, G. ; Montrone, C. ; Skornia, C. ; Wanka, S. ; Rattei, T.* ; Pagel, P. ; Riley, M.L. ; Frishman, D.* ; Surmeli, D. ; Tetko, I.V. ; Oesterheld, M. ; Stuempflen, V. ; Mewes, H.-W.

The mouse functional genome database (MfunGD) :Functional annotation of proteins in the light of their cellular context.

Nucleic Acids Res. 34, D568–D571 (2006)

Shimada, N.* ; Matsudo, H.* ; Osano, K.* ; Arakawa, H. ; Buerstedde, J.-M. ; Matsumoto, Y.* ; Chayahara, K.* ; Torihata, A.* ; Ono, M.*

Activation of the chicken Ig-ß locus by the collaboration of scattered regulatory regions through changes in chromatin structure.

Nucleic Acids Res. 34, 3794-3802 (2006)

Bornkamm, G.W. ; Berens, Ch.* ; Kuklik-Roos, C. ; Bechet, J.-M.* ; Laux, G. ; Bachl, J. ; Korndörfer, M. ; Schlee, M. ; Hölzel, M. ; Malamoussi, A. ; Chapman, R.

Stringent doxycycline-dependent control of gene activities using an episomal one-vector system.

Nucleic Acids Res. 33, 1-11:e137 (2005)

Chen, S.* ; Davies, A.A.* ; Sagan, D. ; Ulrich, H.D.*

The RING finger ATPase Rad5p of Saccharomyces cerevisiae contributes to DNA double-strand break repair in a ubiquitin-independent manner.

Nucleic Acids Res. 33, 5878-5886 (2005)

Döhr, S. ; Klingenhoff, A.* ; Maier, H. ; Hrabě de Angelis, M. ; Werner, T.* ; Schneider, R.

Linking disease-associated genes to regulatory networks via promoter organization.

Nucleic Acids Res. 33, 864-872 (2005)

Güldener, U. ; Münsterkötter, M. ; Kastenmüller, G. ; Strack, N.* ; van Helden, J.* ; Lemer, C.* ; Richelles, J.* ; Wodak, S.J.* ; García-Martínez, J.* ; Pérez-Ortín, J.E.* ; Michael, H.* ; Kaps, A.* ; Talla, E.* ; Dujon, B.* ; André, B.* ; Souciet, J.L.* ; de Montigny, J.* ; Bon, E.* ; Gaillardin, C.* ; Mewes, H.-W.

CYGD: The Comprehensive Yeast Genome Database.

Nucleic Acids Res. 33, SI, D364-368 (2005)

Kasuga, T.* ; Townsend, J.P.* ; Tian, C.* ; Gilbert, L.B.* ; Mannhaupt, G. ; Taylor, J.W.* ; Glass, N.L.*

Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination.

Nucleic Acids Res. 33, 6469-6485 (2005)

Klaften, M. ; Hrabě de Angelis, M.

ARTS: A web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants.

Nucleic Acids Res. 33, 2, W496-W500 (2005)

Lux, Ch. ; Albiez, H.* ; Chapman, R.D. ; Heidinger, M. ; Meininghaus, M. ; Brack-Werner, R. ; Lang, A. ; Ziegler, M. ; Cremer, T. ; Eick, D.

Transition from initiation to promoter proximal pausing requires the CTD of RNA polymerase II.

Nucleic Acids Res. 33, 5139-5144 (2005)

Maier, H. ; Döhr, S. ; Grote, K. ; O'Keeffe, S. ; Werner, T. ; Hrabě de Angelis, M. ; Schneider, R.

LitMiner and WikiGene: Identifying problem-related key players of gene regulation using publication abstracts.

Nucleic Acids Res. 33, 2, W779-W782 (2005)

Riley, M.L. ; Schmidt, T.* ; Wagner, C.* ; Mewes, H.-W. ; Frishman, D.

The PEDANT genome database in 2005.

Nucleic Acids Res. 33, D308-D310 (2005)

Rudd, S.* ; Schoof, H. ; Mayer, K.F.X.

PlantMarkers - a database of predicted molecular markers from plants.

Nucleic Acids Res. 33, 628-632 (2005)

Rudd, S.* ; Tetko, I.V.

Éclair - a web service for unravelling species origin of sequences sampled from mixed host interfaces.

Nucleic Acids Res. 33, 2, W724-W727 (2005)

Andreoli, C. ; Prokisch, H. ; Hörtnagel, K. ; Mueller, J.C. ; Münsterkötter, M. ; Scharfe, C.* ; Meitinger, T.

MitoP2, an integrated databases on mitochondrial proteins in yeast and man.

Nucleic Acids Res. 32, 459-462 (2004)

Chapman, R.D. ; Palancade, B.* ; Lang, A. ; Bensaude, O.* ; Eick, D.

The last CTD repeat of the mammalian RNA polymerase II large subunit is important for its stability.

Nucleic Acids Res. 32, 35-44 (2004)

Mewes, H.-W. ; Amid, C. ; Arnold, R. ; Frishman, D.* ; Güldener, U. ; Mannhaupt, G.* ; Münsterkötter, M. ; Pagel, P. ; Strack, N.* ; Stuempflen, V. ; Warfsmann, J. ; Ruepp, A.

MIPS : analysis and annotation of proteins from whole genomes.

Nucleic Acids Res. 32, D41-D44 (2004)

Ruepp, A. ; Zollner, A.* ; Maier, D.* ; Albermann, K.* ; Hani, J.* ; Mokrejs, M. ; Tetko, I.V. ; Güldener, U. ; Mannhaupt, G. ; Münsterkötter, M. ; Mewes, H.-W.

The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes.

Nucleic Acids Res. 32, 5539-5545 (2004)

Schofield, P.N.* ; Bard, J.B.L.* ; Booth, C.* ; Boniver, J.* ; Covelli, V.* ; Delvenne, P.* ; Ellender, M.* ; Engstrom, W.* ; Goessner, W. ; Gruenberger, M.* ; Höfler, H.

Pathbase: A database of mutant mouse pathology.

Nucleic Acids Res. 32, D512-D515 (2004)

Schoof, H. ; Ernst, R. ; Nazarov, V. ; Pfeifer, L. ; Mewes, H.-W. ; Mayer, K.F.X.

MIPS Arabidopsis thaliana database (MAtDB) An integrated biological knowledge resource for plant genomics.

Nucleic Acids Res. 32, 373-376 (2004)

Bon, E.* ; Casaregola, S.* ; Blandin, G.* ; Llorente, B.* ; Neuvéglise, C.* ; Münsterkötter, M. ; Güldener, U. ; Mewes, H.-W. ; van Helden, J.* ; Dujon, B.* ; Gaillardin, C.*

Molecular evolution of eukaryotic genomes: Hemiascomycetous yeast spliceosomal introns.

Nucleic Acids Res. 31, 1121-1135 (2003)

Drobyshev, A.L. ; Machka, C. ; Horsch, M. ; Seltmann, M. ; Liebscher, V. ; Hrabě de Angelis, M. ; Beckers, J.

Specificity assessment from fractionation experiments (SAFE) : a novel method to evaluate microarray probe specificity based on hybridisation strinencies.

Nucleic Acids Res. 31, 2-10 (2003)

Karlowski, W.M. ; Schoof, H. ; Janakiraman, V. ; Stuempflen, V. ; Mayer, K.F.X.

MOsDB : an integrated information resource for rice genomics.

Nucleic Acids Res. 31, 190-192 (2003)

Schlosser, I. ; Hölzel, M. ; Mürnseer, M. ; Burtscher, H.* ; Weidle, U.H.* ; Eick, D.

A role for c-Myc in the regulation of ribosomal RNA processing.

Nucleic Acids Res. 31, 6148-6156 (2003)

Wolff, H. ; Brack-Werner, R. ; Neumann, M. ; Werner, T. ; Schneider, R.

Integrated functional and bioinformatics approach for the identification and experimental verification of RNA signals : Application to HIV-1 INS.

Nucleic Acids Res. 31, 2839-2851 (2003)

Kiechle, M.* ; Manivasakam, P.* ; Eckardt-Schupp, F. ; Schiestl, R.H.* ; Friedl, A.A.*

Promoter-trapping in Saccharomyces cerevisiae by radiation-assisted fragment insertion.

Nucleic Acids Res. 30:e136 (2002)

Mewes, H.-W. ; Frishman, D. ; Güldener, U. ; Mannhaupt, G. ; Mayer, K.F.X. ; Mokrejs, M. ; Morgenstern, B. ; Münsterkötter, M. ; Rudd, S. ; Weil, B.

MIPS: A database for genomes and protein sequences.

Nucleic Acids Res. 30, 31-34 (2002)

Schoof, H. ; Zaccaria, P. ; Gundlach, H. ; Lemcke, K. ; Rudd, S. ; Kolesov, G. ; Arnold, R. ; Mewes, H.-W. ; Mayer, K.F.X.

MIPS Arabidopsis thaliana Database (MAtDB): An integrated biological konwledge resource based on the first complete plant genome.

Nucleic Acids Res. 30, 91-93 (2002)

Bailly, A.* ; Torres-Padilla, M.E.* ; Tinel, A.P.* ; Weiss, M.C.*

An enhancer element 6 kb upstream of the mouse HNF4alpha1 promoter is activated by glucocorticoids and liver-enriched transcription factors.

Nucleic Acids Res. 29, 3495-3505 (2001)

Lengler, J. ; Krausz, E. ; Tomarev, S.* ; Prescott, A.* ; Quinlan, R.A.* ; Graw, J.

Antagonistic action of Six3 and Prox1 at the ϒ-crystallin promoter.

Nucleic Acids Res. 29, 515-526 (2001)

Schneider, R.* ; Lurz, R.* ; Lüder, G.* ; Tolksdorf, C.* ; Travers, A.* ; Muskhelishvili, G.*

An architectural role of the Escherichia coli chromatin protein FIS in organising DNA.

Nucleic Acids Res. 29, 5107-5114 (2001)

Scharfe, C.* ; Zaccaria, P. ; Hoertnagel, K.* ; Jaksch, M.* ; Klopstock, T.* ; Dembowski, M.* ; Lill, R.* ; Prokisch, H.* ; Gerbitz, K.D.* ; Neupert, W.* ; Mewes, H.-W. ; Meitinger, T.*

MITOP, the mitochondrial proteome database: 2000 update.

Nucleic Acids Res. 28, 155-158 (2000)

Wittekindt, N.E. ; Hörtnagel, K. ; Geltinger, C.

Activation of c-myc promoter P1 by immunoglobulin κ gene enhancers in Burkitt lymphoma: functional characterization of the intron enhancer motifs kB, E box 1 and E box 2 and of the 3' enhancer motif PU.

Nucleic Acids Res. 28, 800-808 (2000)

Immervoll, T. ; Wjst, M.

Current status of the asthma and allergy database.

Nucleic Acids Res. 27, 213-214 (1999)

Brielmeier, M. ; Bechet, J.-M.* ; Falk, M.H.* ; Pawlita, M.* ; Polack, A. ; Bornkamm, G.W.

Improving stable transfection efficiency : antioxidants dramatically improve the outgrowth of clones under dominant marker selection.

Nucleic Acids Res. 26, 2082-2085 (1998)

Frech, K. ; Herrmann, G. ; Werner, T.