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2018

Deciphering human ribonucleoprotein regulatory networks.
Mukherjee, N. and Wessels, H.H. and Lebedeva, S. and Sajek, M. and Ghanbari, M. and Garzia, A. and Munteanu, A. and Yusuf, D. and Farazi, T. and Hoell, J.I. and Akat, K.M. and Akalin, A. and Tuschl, T. and Ohler, U.
Nucleic Acids Research 5 December 2018 (In Press)

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Szklarczyk, D. and Gable, A.L. and Lyon, D. and Junge, A. and Wyder, S. and Huerta-Cepas, J. and Simonovic, M. and Doncheva, N.T. and Morris, J.H. and Bork, P. and Jensen, L.J. and von Mering, C.
Nucleic Acids Research 22 November 2018 (In Press)

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas, J. and Szklarczyk, D. and Heller, D. and Hernández-Plaza, A. and Forslund, S.K. and Cook, H. and Mende, D.R. and Letunic, I. and Rattei, T. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 12 November 2018 (In Press)

ProTox-II: a webserver for the prediction of toxicity of chemicals.
Banerjee, P. and Eckert, A.O. and Schrey, A.K. and Preissner, R.
Nucleic Acids Research 46 (W1): W257-W263. 2 July 2018

MetExplore: collaborative edition and exploration of metabolic networks.
Cottret, L. and Frainay, C. and Chazalviel, M. and Cabanettes, F. and Gloaguen, Y. and Camenen, E. and Merlet, B. and Heux, S. and Portais, J.C. and Poupin, N. and Vinson, F. and Jourdan, F.
Nucleic Acids Research 46 (W1): W495-W502. 2 July 2018

iPath3.0: interactive pathways explorer v3.
Darzi, Y. and Letunic, I. and Bork, P. and Yamada, T.
Nucleic Acids Research 46 (W1): W510-W513. 2 July 2018

Molecular basis of titin exon exclusion by RBM20 and the novel titin splice regulator PTB4.
Dauksaite, V. and Gotthardt, M.
Nucleic Acids Research 46 (10): 5227-5238. 1 June 2018

The IL-4/STAT6/PPARγ signaling axis is driving the expansion of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages.
Daniel, B. and Nagy, G. and Horvath, A. and Czimmerer, Z. and Cuaranta-Monroy, I. and Poliska, S. and Hays, T.T. and Sauer, S. and Francois-Deleuze, J. and Nagy, L.
Nucleic Acids Research 46 (9): 4425-4439. 18 May 2018

Structural basis of gene regulation by the Grainyhead/CP2 transcription factor family.
Ming, Q. and Roske, Y. and Schuetz, A. and Walentin, K. and Ibraimi, I. and Schmidt-Ott, K.M. and Heinemann, U.
Nucleic Acids Research 46 (4): 2082-2095. 28 February 2018

MVP: a microbe-phage interaction database.
Gao, N.L. and Zhang, C. and Zhang, Z. and Hu, S. and Lercher, M.J. and Zhao, X.M. and Bork, P. and Liu, Z. and Chen, W.H.
Nucleic Acids Research 46 (D1): D700-D707. 4 January 2018

mVOC 2.0: a database of microbial volatiles.
Lemfack, M.C. and Gohlke, B.O. and Toguem, S.M.T. and Preissner, S. and Piechulla, B. and Preissner, R.
Nucleic Acids Research 46 (D1): D1261-D1265. 4 January 2018

SuperDRUG2: a one stop resource for approved/marketed drugs.
Siramshetty, V.B. and Eckert, O.A. and Gohlke, B.O. and Goede, A. and Chen, Q. and Devarakonda, P. and Preissner, S. and Preissner, R.
Nucleic Acids Research 46 (D1): D1137-D1143. 4 January 2018

2017

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.
Heller, D. and Krestel, R. and Ohler, U. and Vingron, M. and Marsico, A.
Nucleic Acids Research 45 (19): 11004-11018. 2 November 2017

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
Grüning, B.A. and Fallmann, J. and Yusuf, D. and Will, S. and Erxleben, A. and Eggenhofer, F. and Houwaart, T. and Batut, B. and Videm, P. and Bagnacani, A. and Wolfien, M. and Lott, S.C. and Hoogstrate, Y. and Hess, W.R. and Wolkenhauer, O. and Hoffmann, S. and Akalin, A. and Ohler, U. and Stadler, P.F. and Backofen, R.
Nucleic Acids Research 45 (W1): W560-W566. 3 July 2017

GPCR-SSFE 2.0: a fragment-based molecular modeling web tool for Class A G-protein coupled receptors.
Worth, C.L. and Kreuchwig, F. and Tiemann, J.K.S. and Kreuchwig, A. and Ritschel, M. and Kleinau, G. and Hildebrand, P.W. and Krause, G.
Nucleic Acids Research 45 (W1): W408-W415. 3 July 2017

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Uyar, B. and Yusuf, D. and Wurmus, R. and Rajewsky, N. and Ohler, U. and Akalin, A.
Nucleic Acids Research 45 (10): e91. 2 June 2017

Recognition but no repair of abasic site in single-stranded DNA by human ribosomal uS3 protein residing within intact 40S subunit.
Grosheva, A.S. and Zharkov, D.O. and Stahl, J. and Gopanenko, Al.V. and Tupikin, A.E. and Kabilov, M.R. and Graifer, D.M. and Karpova, G.G.
Nucleic Acids Research 45 (7): 3833-3843. 20 April 2017

Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution.
Mauri, M. and Kirchner, M. and Aharoni, R. and Ciolli Mattioli, C. and van den Bruck, D. and Gutkovitch, N. and Modepalli, V. and Selbach, M. and Moran, Y. and Chekulaeva, M.
Nucleic Acids Research 45 (2): 938-950. 25 January 2017

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.
Schmidt, F. and Gasparoni, N. and Gasparoni, G. and Gianmoena, K. and Cadenas, C. and Polansky, J.K. and Ebert, P. and Nordstroem, K. and Barann, M. and Sinha, A. and Froehler, S. and Xiong, J. and Dehghani Amirabad, A. and Behjati Ardakani, F. and Hutter, B. and Zipprich, G. and Felder, B. and Eils, J. and Brors, B. and Chen, W. and Hengstler, J.G. and Hamann, A. and Lengauer, T. and Rosenstiel, P. and Walter, J. and Schulz, M.H.
Nucleic Acids Research 45 (1): 54-66. 9 January 2017

Regulated complex assembly safeguards the fidelity of Sleeping Beauty transposition.
Wang, Y. and Pryputniewicz-Dobrinska, D. and Nagy, E.E. and Kaufman, C.D. and Singh, M. and Yant, S. and Wang, J. and Dalda, A. and Kay, M.A. and Ivics, Z. and Izsvák, Z.
Nucleic Acids Research 45 (1): 311-326. 9 January 2017

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.
Chen, W.H. and Lu, G. and Chen, X. and Zhao, X.M. and Bork, P.
Nucleic Acids Research 45 (D1): D940-D944. 4 January 2017

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Mende, D.R. and Letunic, I. and Huerta-Cepas, J. and Li, S.S. and Forslund, K. and Sunagawa, S. and Bork, P.
Nucleic Acids Research 45 (D1): D529-D534. 4 January 2017

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Szklarczyk, D. and Morris, J.H. and Cook, H. and Kuhn, M. and Wyder, S. and Simonovic, M. and Santos, A. and Doncheva, N.T. and Roth, A. and Bork, P. and Jensen, L.J. and von Mering, C.
Nucleic Acids Research 45 (D1): D362-D368. 4 January 2017

2016

G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-hairpin-duplex switch.
Kaplan, O.I. and Berber, B. and Hekim, N. and Doluca, O.
Nucleic Acids Research 44 (19): 9083-9095. 2 November 2016

Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements.
Telorac, J. and Prykhozhij, S.V. and Schöne, S. and Meierhofer, D. and Sauer, S. and Thomas-Chollier, M. and Meijsing, S.H.
Nucleic Acids Research 44 (13): 6142-6156. 27 July 2016

SL2: an interactive webtool for modeling of missing segments in proteins.
Ismer, J. and Rose, A.S. and Tiemann, J.K.S. and Goede, A. and Preissner, R. and Hildebrand, P.W.
Nucleic Acids Research 44 (W1): W390-W394. 8 July 2016

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
Letunic, I. and Bork, P.
Nucleic Acids Research 44 (W1): W242-W245. 8 July 2016

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz, R.F. and Tamuri, A.U. and Kultys, M. and King, J. and Godwin, J. and Florescu, A.M. and Schultz, J. and Goldman, N.
Nucleic Acids Research 44 (8): e77. 5 May 2016

A comprehensive comparison of general RNA-RNA interaction prediction methods.
Lai, D. and Meyer, I.M.
Nucleic Acids Research 44 (7): e61. 20 April 2016

Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA.
Cui, H. and Schlesinger, J. and Schoenhals, S. and Toenjes, M. and Dunkel, I. and Meierhofer, D. and Cano, E. and Schulz, K. and Berger, M.F. and Haack, T. and Abdelilah-Seyfried, S. and Bulyk, M.L. and Sauer, S. and Sperling, S.R.
Nucleic Acids Research 44 (6): 2538-2553. 7 April 2016

Integration of multi-omics data of a genome-reduced bacterium: prevalence of post-transcriptional regulation and its correlation with protein abundances.
Chen, W.H. and van Noort, V. and Lluch-Senar, M. and Hennrich, M.L. and Wodke, J.A.H. and Yus, E. and Alibes, A. and Roma, G. and Mende, D.R. and Pesavento, C. and Typas, A. and Gavin, A.C. and Serrano, L. and Bork, P.
Nucleic Acids Research 44 (3): 1192-1202. 18 February 2016

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

Nucleic Acids Research 44 (D1): D27-D37. 4 January 2016

CancerResource - updated database of cancer-relevant proteins, mutations and interacting drugs.
Gohlke, B.O. and Nickel, J. and Otto, R. and Dunkel, M. and Preissner, R.
Nucleic Acids Research 44 (D1): D932-D937. 4 January 2016

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Huerta-Cepas, J. and Szklarczyk, D. and Forslund, K. and Cook, H. and Heller, D. and Walter, M.C. and Rattei, T. and Mende, D.R. and Sunagawa, S. and Kuhn, M. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 44 (D1): D286-D293. 4 January 2016

The SIDER database of drugs and side effects.
Kuhn, M. and Letunic, I. and Jensen, L.J. and Bork, P.
Nucleic Acids Research 44 (D1): D1075-D1079. 4 January 2016

WITHDRAWN-a resource for withdrawn and discontinued drugs.
Siramshetty, V.B. and Nickel, J. and Omieczynski, C. and Gohlke, B.O. and Drwal, M.N. and Preissner, R.
Nucleic Acids Research 44 (D1): D1080-D1086. 4 January 2016

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Szklarczyk, D. and Santos, A. and von Mering, C. and Jensen, L.J. and Bork, P. and Kuhn, M.
Nucleic Acids Research 44 (D1): D380-D384. 4 January 2016

2015

Development of an intein-mediated split-Cas9 system for gene therapy.
Truong, D.J.J. and Kühner, K. and Kühn, R. and Werfel, S. and Engelhardt, S. and Wurst, W. and Ortiz, O.
Nucleic Acids Research 43 (13): 6450-6458. 27 July 2015

Development of a high-resolution NGS-based HLA-typing and analysis pipeline.
Wittig, M. and Anmarkrud, J.A. and Kässens, J.C. and Koch, S. and Forster, M. and Ellinghaus, E. and Hov, J.R. and Sauer, S. and Schimmler, M. and Ziemann, M. and Görg, S. and Jacob, F. and Karlsen, T.H. and Franke, A.
Nucleic Acids Research 43 (11): e70. 23 June 2015

Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum.
Staudacher, J.J. and Naarmann-de Vries, I.S. and Ujvari, S.J. and Klinger, B. and Kasim, M. and Benko, E. and Ostareck-Lederer, A. and Ostareck, D.H. and Bondke Persson, A. and Lorenzen, S. and Meier, J.C. and Bluethgen, N. and Persson, P.B. and Henrion-Caude, A. and Mrowka, R. and Faehling, M.
Nucleic Acids Research 43 (6): 3219-3236. 31 March 2015

Super natural II -a database of natural products.
Banerjee, P. and Erehman, J. and Gohlke, B.O. and Wilhelm, T. and Preissner, R. and Dunkel, M.
Nucleic Acids Research 43 (Database issue): D935-D939. 28 January 2015

DoRiNA 2.0-upgrading the doRiNA database of RNA interactions in post-transcriptional regulation.
Blin, K. and Dieterich, C. and Wurmus, R. and Rajewsky, N. and Landthaler, M. and Akalin, A.
Nucleic Acids Research 43 (Database issue): D160-D167. 28 January 2015

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Minguez, P. and Letunic, I. and Parca, L. and Garcia-Alonso, L. and Dopazo, J. and Huerta-Cepas, J. and Bork, P.
Nucleic Acids Research 43 (Database issue): D494-D502. 28 January 2015

STRING v10: protein-protein interaction networks, integrated over the tree of life.
Szklarczyk, D. and Franceschini, A. and Wyder, S. and Forslund, K. and Heller, D. and Huerta-Cepas, J. and Simonovic, M. and Roth, A. and Santos, A. and Tsafou, K.P. and Kuhn, M. and Bork, P. and Jensen, L.J. and von Mering, C.
Nucleic Acids Research 43 (D1): D447-D452. January 2015

2014

Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models.
Maaskola, J. and Rajewsky, N.
Nucleic Acids Research 42 (21): 12995-13011. 1 December 2014

Modes of TAL effector-mediated repression.
Werner, J. and Gossen, M.
Nucleic Acids Research 42 (21): 13061-13073. 1 December 2014

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.
Yardımcı, G.G. and Frank, C.L. and Crawford, G.E. and Ohler, U.
Nucleic Acids Research 42 (19): 11865-11878. 29 October 2014

Alkemio: association of chemicals with biomedical topics by text and data mining.
Gijon-Correas, J.A. and Andrade-Navarro, M.A. and Fontaine, J.F.
Nucleic Acids Research 42 (W1): W422-W429. 1 July 2014

e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation.
Lai, D. and Meyer, I.M.
Nucleic Acids Research 42 (Web Server issue): W373-W376. 1 July 2014

COUGER-co-factors associated with uniquely-bound genomic regions.
Munteanu, A. and Ohler, U. and Gordân, R.
Nucleic Acids Research 42 (Web Server issue): W461-W467. July 2014

Similarity in targets with REST points to neural and glioblastoma related miRNAs.
Gebhardt, M.L. and Reuter, S. and Mrowka, R. and Andrade-Navarro, M.A.
Nucleic Acids Research 42 (9): 5436-5446. 14 May 2014

Structural insights into RNA encapsidation and helical assembly of the Toscana virus nucleoprotein.
Olal, D. and Dick, A. and Woods, V.L. and Liu, T. and Li, S. and Devignot, S. and Weber, F. and Saphire, E.O. and Daumke, O.
Nucleic Acids Research 42 (9): 6025-6037. 14 May 2014

The Transformer database: biotransformation of xenobiotics.
Hoffmann, M.F. and Preissner, S.C. and Nickel, J. and Dunkel, M. and Preissner, R. and Preissner, S.
Nucleic Acids Research 42 (1): D1113-D1117. 1 January 2014

STITCH 4: integration of protein-chemical interactions with user data.
Kuhn, M. and Szklarczyk, D. and Pletscher-Frankild, S. and Blicher, T.H. and von Mering, C. and Jensen, L.J. and Bork, P.
Nucleic Acids Research 42 (1): D401-D407. 1 January 2014

mVOC: a database of microbial volatiles.
Lemfack, M.C. and Nickel, J. and Dunkel, M. and Preissner, R. and Piechulla, B.
Nucleic Acids Research 42 (1): D744-D748. 1 January 2014

eggNOG v4.0: nested orthology inference across 3686 organisms.
Powell, S. and Forslund, K. and Szklarczyk, D. and Trachana, K. and Roth, A. and Huerta-Cepas, J. and Gabaldon, T. and Rattei, T. and Creevey, C. and Kuhn, M. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 42 (1): D231-D239. 1 January 2014

CellFinder: a cell data repository.
Stachelscheid, H. and Seltmann, S. and Lekschas, F. and Fontaine, J.F. and Mah, N. and Neves, M. and Andrade-Navarro, M.A. and Leser, U. and Kurtz, A.
Nucleic Acids Research 42 (1): D950-D958. 1 January 2014

uORFdb - a comprehensive literature database on eukaryotic uORF biology.
Wethmar, K. and Barbosa-Silva, A. and Andrade-Navarro, M.A. and Leutz, A.
Nucleic Acids Research 42 (1): D60-D67. 1 January 2014

2013

Transient RNA structure features are evolutionarily conserved and can be computationally predicted.
Zhu, J.Y.A. and Steif, A. and Proctor, J.R. and Meyer, I.M.
Nucleic Acids Research 41 (12): 6273-6285. 8 July 2013

MYCN and HDAC2 cooperate to repress miR-183 signaling in neuroblastoma.
Lodrini, M. and Oehme, I. and Schroeder, C. and Milde, T. and Schier, M.C. and Kopp-Schneider, A. and Schulte, J.H. and Fischer, M. and De Preter, K. and Pattyn, F. and Castoldi, M. and Muckenthaler, M.U. and Kulozik, A.E. and Westermann, F. and Witt, O. and Deubzer, H.E.
Nucleic Acids Research 41 (12): 6018-6033. 1 July 2013

Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1.
Pham, T.H. and Minderjahn, J. and Schmidl, C. and Hoffmeister, H. and Schmidhofer, S. and Chen, W. and Laengst, G. and Benner, C. and Rehli, M.
Nucleic Acids Research 41 (13): 6391-6402. July 2013

COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.
Proctor, J.R. and Meyer, I.M.
Nucleic Acids Research 41 (9): e102. May 2013

Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells.
Feldmann, R. and Fischer, C. and Kodelja, V. and Behrens, S. and Haas, S. and Vingron, M. and Timmermann, B. and Geikowski, A. and Sauer, S.
Nucleic Acids Research 41 (6): 3518-3531. April 2013

Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.
Li, N. and You, X. and Chen, T. and Mackowiak, S.D. and Friedlaender, M.R. and Weigt, M. and Du, H. and Gogol-Doering, A. and Chang, Z. and Dieterich, C. and Hu, Y. and Chen, W.
Nucleic Acids Research 41 (6): 3619-3634. 8 February 2013

Sleeping Beauty transposon-based system for cellular reprogramming and targeted gene insertion in induced pluripotent stem cells.
Grabundzija, I. and Wang, J. and Sebe, A. and Erdei, Z. and Kajdi, R. and Devaraj, A. and Steinemann, D. and Szuhai, K. and Stein, U. and Cantz, T. and Schambach, A. and Baum, C. and Izsvák, Z. and Sarkadi, B. and Ivics, Z.
Nucleic Acids Research 41 (3): 1829-1847. 1 February 2013

Patterns of methylation heritability in a genome-wide analysis of four brain regions.
Quon, G. and Lippert, C. and Heckerman, D. and Listgarten, J.
Nucleic Acids Research 41 (4): 2095-2104. 1 February 2013

Development and application of a DNA microarray-based yeast two-hybrid system.
Suter, B. and Fontaine, J.F. and Yildirimman, R. and Raskó, T. and Schaefer, M.H. and Rasche, A. and Porras, P. and Vázquez-Álvarez, B.M. and Russ, J. and Rau, K. and Foulle, R. and Zenkner, M. and Saar, K. and Herwig, R. and Andrade-Navarro, M.A. and Wanker, E.E.
Nucleic Acids Research 41 (3): 1496-507. 1 February 2013

STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Franceschini, A. and Szklarczyk, D. and Frankild, S. and Kuhn, M. and Simonovic, M. and Roth, A. and Lin, J. and Minguez, P. and Bork, P. and von Mering, C. and Jensen, L.J.
Nucleic Acids Research 41 (D1): D808-D815. 1 January 2013

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins.
Minguez, P. and Letunic, I. and Parca, L. and Bork, P.
Nucleic Acids Research 41 (D1): D306-D311. 1 January 2013

SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations.
von Eichborn, J. and Dunkel, M. and Gohlke, B.O. and Preissner, S.C. and Hoffmann, M.F. and Bauer, J.M.J. and Armstrong, J.D. and Schaefer, M.H. and Andrade-Navarro, M.A. and Le Novere, N. and Croning, M.D.R. and Grant, S.G.N. and van Nierop, P. and Smit, A.B. and Preissner, R.
Nucleic Acids Research 41 (D1): D834-D840. 1 January 2013

2012

Retargeting transposon insertions by the adeno-associated virus Rep protein.
Ammar, I. and Gogol-Doering, A. and Miskey, C. and Chen, W. and Cathomen, T. and Izsvak, Z. and Ivics, Z.
Nucleic Acids Research 40 (14): 6693-6712. 1 August 2012

The Lin28 cold-shock domain remodels pre-let-7 microRNA.
Mayr, F. and Schütz, A. and Dge, N. and Heinemann, U.
Nucleic Acids Research 40 (15): 7492-7506. 1 August 2012

R-CHIE: a web server and R package for visualizing RNA secondary structures.
Lai, D. and Proctor, J.R. and Zhu, J.Y.A. and Meyer, I.M.
Nucleic Acids Research 40 (12): e95. July 2012

Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks.
Schaefer, M.H. and Wanker, E.E. and Andrade-Navarro, M.A.
Nucleic Acids Research 40 (10): 4273-4287. 1 May 2012

Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts.
Zhelyazkova, P. and Hammani, K. and Rojas, M. and Voelker, R. and Vargas-Suarez, M. and Boerner, T. and Barkan, A.
Nucleic Acids Research 40 (7): 3092-3105. 1 April 2012

Histone hypoacetylation is required to maintain late replication timing of constitutive heterochromatin.
Casas-Delucchi, C.S. and van Bemmel, J.G. and Haase, S. and Herce, H.D. and Nowak, D. and Meilinger, D. and Stear, J.H. and Leonhardt, H. and Cardoso, M.C.
Nucleic Acids Research 40 (1): 159-169. 1 January 2012

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.
Friedlaender, M.R. and Mackowiak, S.D. and Li, N. and Chen, W. and Rajewsky, N.
Nucleic Acids Research 40 (1): 37-52. 1 January 2012

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Powell, S. and Szklarczyk, D. and Trachana, K. and Roth, A. and Kuhn, M. and Muller, J. and Arnold, R. and Rattei, T. and Letunic, I. and Doerks, T. and Jensen, L.J. and von Mering, C. and Bork, P.
Nucleic Acids Research 40 (D1): D284-D289. 1 January 2012

The Pfam protein families database.
Punta, M. and Coggill, P.C. and Eberhardt, R.Y. and Mistry, J. and Tate, J. and Boursnell, C. and Pang, N. and Forslund, K. and Ceric, G. and Clements, J. and Heger, A. and Holm, L. and Sonnhammer, E.L.L. and Eddy, S.R. and Bateman, A. and Finn, R.D.
Nucleic Acids Research 40 (D1): D290-D301. 1 January 2012

doRiNA: a database of RNA interactions in post-transcriptional regulation.
Anders, G. and Mackowiak, S.D. and Jens, M. and Maaskola, J. and Kuntzagk, A. and Rajewsky, N. and Landthaler, M. and Dieterich, C.
Nucleic Acids Research 40 (1): D180-D186. January 2012

OGEE: an online gene essentiality database.
Chen, W.H. and Minguez, P. and Lercher, M.J. and Bork, P.
Nucleic Acids Research 40 (Database issue): D901-D906. January 2012

STITCH 3: zooming in on protein-chemical interactions.
Kuhn, M. and Szklarczyk, D. and Franceschini, A. and von Mering, C. and Jensen, L.J. and Bork, P.
Nucleic Acids Research 40 (Database Issue): D876-D880. January 2012

NF-κB regulates DNA double-strand break repair in conjunction with BRCA1-CtIP complexes.
Volcic, M. and Karl, S. and Baumann, B. and Salles, D. and Daniel, P. and Fulda, S. and Wiesmueller, L.
Nucleic Acids Research 40 (1): 181-195. January 2012

2011

The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA.
Leu, K. and Obermayer, B. and Rajamani, S. and Gerland, U. and Chen, I.A.
Nucleic Acids Research 39 (18): 8135-8147. October 2011

Avoiding cytotoxicity of transposases by dose-controlled mRNA delivery.
Galla, M. and Schambach, A. and Falk, C.S. and Maetzig, T. and Kuehle, J. and Lange, K. and Zychlinski, D. and Heinz, N. and Brugman, M.H. and Goehring, G. and Izsvak, Z. and Ivics, Z. and Baum, C.
Nucleic Acids Research 39 (16): 7147-7160. 1 September 2011

3D-image analysis platform monitoring relocation of pluripotency genes during reprogramming.
Jost, K.L. and Haase, S. and Smeets, D. and Schrode, N. and Schmiedel, J.M. and Bertulat, B. and Herzel, H. and Cremer, M. and Cardoso, M.C.
Nucleic Acids Research 39 (17): e113. 1 September 2011

Widespread expression of piRNA-like molecules in somatic tissues.
Yan, Z. and Hu, H.Y. and Jiang, X. and Maierhofer, V. and Neb, E. and He, L. and Hu, Y. and Hu, H. and Li, N. and Chen, W. and Khaitovich, P.
Nucleic Acids Research 39 (15): 6596-6607. 1 August 2011

SDM - a server for predicting effects of mutations on protein stability and malfunction.
Worth, C.L. and Preissner, R. and Blundell, T.L.
Nucleic Acids Research 39 (Suppl. 2): W215-W222. 1 July 2011

Genie: literature-based gene prioritization at multi genomic scale.
Fontaine, J.F. and Priller, F. and Barbosa-Silva, A. and Andrade-Navarro, M.A.
Nucleic Acids Research 39 (Suppl 2): W455-W461. July 2011

The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons.
Muro, E.M. and Mah, N. and Moreno-Hagelsieb, G. and Andrade-Navarro, M.A.
Nucleic Acids Research 39 (5): 1732-1738. 1 March 2011

SuperSweet - a resource on natural and artificial sweetening agents.
Ahmed, J. and Preissner, S. and Dunkel, M. and Worth, C.L. and Eckert, A. and Preissner, R.
Nucleic Acids Research 39 (Suppl. 1): D377-D382. 1 January 2011

FragmentStore - a comprehensive database of fragments linking metabolites, toxic molecules and drugs.
Ahmed, J. and Worth, C.L. and Thaben, P. and Matzig, C. and Blasse, C. and Dunkel, M. and Preissner, R.
Nucleic Acids Research 39 (Suppl. 1): D1049-D1054. 1 January 2011

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Szklarczyk, D. and Franceschini, A. and Kuhn, M. and Simonovic, M. and Roth, A. and Minguez, P. and Doerks, T. and Stark, M. and Muller, J. and Bork, P. and Jensen, L.J. and von Mering, C.
Nucleic Acids Research 39 (Database issue): D561-D568. January 2011

2010

A network of conserved co-occurring motifs for the regulation of alternative splicing.
Suyama, M. and Harrington, E.D. and Vinokourova, S. and von Knebel Doeberitz, M. and Ohara, O. and Bork, P.
Nucleic Acids Research 38 (22): 7916-7926. 1 December 2010

The GW/WG repeats of Drosophila GW182 function as effector motifs for miRNA-mediated repression.
Chekulaeva, M. and Parker, R. and Filipowicz, W.
Nucleic Acids Research 38 (19): 6673-6683. October 2010

Efficient conditional and promoter-specific in vivo expression of cDNAs of choice by taking advantage of recombinase-mediated cassette exchange using FlEx gene traps.
Schebelle, L. and Wolf, C. and Stribl, C. and Javaheri, T. and Schnuetgen, F. and Ettinger, A. and Ivics, Z. and Hansen, J. and Ruiz, P. and von Melchner, H. and Wurst, W. and Floss, T.
Nucleic Acids Research 38 (9): e106. May 2010

Measurement of replication structures at the nanometer scale using super-resolution light microscopy.
Baddeley, D. and Chagin, V.O. and Schermelleh, L. and Martin, S. and Pombo, A. and Carlton, P.M. and Gahl, A. and Domaing, P. and Birk, U. and Leonhardt, H. and Cremers, C.W. and Cardoso, M.C.
Nucleic Acids Research 38 (2): e8. March 2010

The Pfam protein families database.
Finn, R.D. and Mistry, J. and Tate, J. and Coggill, P. and Heger, A. and Pollington, J.E. and Gavin, O.L. and Gunasekaran, P. and Ceric, G. and Forslund, K. and Holm, L. and Sonnhammer, E.L.L. and Eddy, S.R. and Bateman, A.
Nucleic Acids Research 38 (Suppl 1): D211-D222. 1 January 2010

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
Ostlund, G. and Schmitt, T. and Forslund, K. and Köstler, T. and Messina, D.N. and Roopra, S. and Frings, O. and Sonnhammer, E.L.L.
Nucleic Acids Research 38 (Suppl 1): D196-D203. 1 January 2010

The ITS2 Database III-sequences and structures for phylogeny.
Koetschan, C. and Foerster, F. and Keller, A. and Schleicher, T. and Ruderisch, B. and Schwarz, R. and Mueller, T. and Wolf, M. and Schultz, J.
Nucleic Acids Research 38 (Suppl 1): D275-D279. January 2010

STITCH 2: an interaction network database for small molecules and proteins.
Kuhn, M. and Szklarczyk, D. and Franceschini, A. and Campillos, M. and von Mering, C. and Jensen, L.J. and Beyer, A. and Bork, P.
Nucleic Acids Research 38 (Database issue): D552-D556. January 2010

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Muller, J. and Szklarczyk, D. and Julien, P. and Letunic, I. and Roth, A. and Kuhn, M. and Powell, S. and von Mering, C. and Doerks, T. and Jensen, L.J. and Bork, P.
Nucleic Acids Research 38 (Database issue): D190-D195. January 2010

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.
Woerner, S.M. and Yuan, Y.P. and Benner, A. and Korff, S. and von Knebel Doeberitz, M. and Bork, P.
Nucleic Acids Research 38 (Database issue): D682-D689. January 2010

2009

HMMCONVERTER 1.0: a toolbox for hidden Markov models.
Lam, T.Y. and Meyer, I.M.
Nucleic Acids Research 37 (21): e139. November 2009

Detecting species-site dependencies in large multiple sequence alignments.
Schwarz, R. and Seibel, P.N. and Rahmann, S. and Schoen, C. and Huenerberg, M. and Mueller-Reible, C. and Dandekar, T. and Karchin, R. and Schultz, J. and Mueller, T.
Nucleic Acids Research 37 (18): 5959-5968. October 2009

MedlineRanker: flexible ranking of biomedical literature.
Fontaine, J.F. and Barbosa-Silva, A. and Schaefer, M. and Huska, M.R. and Muro, E.M. and Andrade-Navarro, M.A.
Nucleic Acids Research 37 (Web Server Issue): W141-W146. 1 July 2009

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships.
Yokoyama, K.D. and Ohler, U. and Wray, G.A.
Nucleic Acids Research 37 (13): e92. July 2009

Crystal structure of KorA bound to operator DNA: insight into repressor cooperation in RP4 gene regulation.
Koenig, B. and Mueller, J.J. and Lanka, E. and Heinemann, U.
Nucleic Acids Research 37 (6): 1915-1924. April 2009

Inducible expression of coding and inhibitory RNAs from retargetable genomic loci.
Weidenfeld, I. and Gossen, M. and Loew, R. and Kentner, D. and Berger, S. and Goerlich, D. and Bartsch, D. and Bujard, H. and Schoenig, K.
Nucleic Acids Research 37 (7): e50. April 2009

Positioning of subdomain IIId and apical loop of domain II of the hepatitis C IRES on the human 40S ribosome.
Babaylova, E. and Graifer, D. and Malygin, A. and Stahl, J. and Shatsky, I. and Karpova, G.
Nucleic Acids Research 37 (4): 1141-1151. March 2009

A versatile non-radioactive assay for DNA methyltransferase activity and DNA binding.
Frauer, C. and Leonhardt, H.
Nucleic Acids Research 37 (3): e22. February 2009

UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome.
Chaurasia, G. and Malhotra, S. and Russ, J. and Schnoegl, S. and Haenig, C. and Wanker, E.E. and Futschik, M.E.
Nucleic Acids Research 37 (Database Issue): D657-D660. January 2009

InterPro: the integrative protein signature database.
Hunter, S. and Apweiler, R. and Attwood, T.K. and Bairoch, A. and Bateman, A. and Binns, D. and Bork, P. and Das, U. and Daugherty, L. and Duquenne, L. and Finn, R.D. and Gough, J. and Haft, D. and Hulo, N. and Kahn, D. and Kelly, E. and Laugraud, A. and Letunic, I. and Lonsdale, D. and Lopez, R. and Madera, M. and Maslen, J. and McAnulla, C. and McDowall, J. and Mistry, J. and Mitchell, A. and Mulder, N. and Natale, D. and Orengo, C. and Quinn, A.F. and Selengut, J.D. and Sigrist, C.J. and Thimma, M. and Thomas, P.D. and Valentin, F. and Wilson, D. and Wu, C.H. and Yeats, C.
Nucleic Acids Research 37 (Database Issue): D211-D215. January 2009

STRING 8--a global view on proteins and their functional interactions in 630 organisms.
Jensen, L.J. and Kuhn, M. and Stark, M. and Chaffron, S. and Creevey, C. and Muller, J. and Doerks, T. and Julien, P. and Roth, A. and Simonovic, M. and Bork, P. and von Mering, C.
Nucleic Acids Research 37 (Database Issue): D412-D416. January 2009

SMART 6: recent updates and new developments.
Letunic, I. and Doerks, T. and Bork, P.
Nucleic Acids Research 37 (Database Issue): D229-D232. January 2009

2008

Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis.
Schoening, J.C. and Streitner, C. and Meyer, I.M. and Gao, Y. and Staiger, D.
Nucleic Acids Research 36 (22): 6977-6987. December 2008

Homogeneity and persistence of transgene expression by omitting antibiotic selection in cell line isolation.
Kaufman, W.L. and Kocman, I. and Agrawal, V. and Rahn, H.P. and Besser, D. and Gossen, M.
Nucleic Acids Research 36 (17): e111. October 2008

KEGG Atlas mapping for global analysis of metabolic pathways.
Okuda, S. and Yamada, T. and Hamajima, M. and Itoh, M. and Katayama, T. and Bork, P. and Goto, S. and Kanehisa, M.
Nucleic Acids Research 36 (Web Server Issue): W423-W426. 1 July 2008

The Pfam protein families database.
Finn, R.D. and Tate, J. and Mistry, J. and Coggill, P.C. and Sammut, S.J. and Hotz, H.R. and Ceric, G. and Forslund, K. and Eddy, S.R. and Sonnhammer, E.L.L. and Bateman, A.
Nucleic Acids Research 36 (Suppl 1): D281-D288. 1 January 2008

SuperTarget and Matador: resources for exploring drug-target relationships.
Guenther, S. and Kuhn, M. and Dunkel, M. and Campillos, M. and Senger, C. and Petsalaki, E. and Ahmed, J. and Urdiales, E.G. and Gewiess, A. and Jensen, L.J. and Schneider, R. and Skoblo, R. and Russell, R.B. and Bourne, P.E. and Bork, P. and Preissner, R.
Nucleic Acids Research 36 (Database issue): D919-D922. January 2008

4DXpress: a database for cross-species expression pattern comparisons.
Haudry, Y. and Berube, H. and Letunic, I. and Weeber, P.D. and Gagneur, J. and Girardot, C. and Kapushesky, M. and Arendt, D. and Bork, P. and Brazma, A. and Furlong, E.E. and Wittbrodt, J. and Henrich, T.
Nucleic Acids Research 36 (Database issue): D847-D853. January 2008

eggNOG: automated construction and annotation of orthologous groups of genes.
Jensen, L.J. and Julien, P. and Kuhn, M. and von Mering, C. and Muller, J. and Doerks, T. and Bork, P.
Nucleic Acids Research 36 (Database issue): D250-D254. January 2008

STITCH: interaction networks of chemicals and proteins.
Kuhn, M. and von Mering, C. and Campillos, M. and Jensen, L.J. and Bork, P.
Nucleic Acids Research 36 (Database issue): D684-D688. January 2008

NetworKIN: a resource for exploring cellular phosphorylation networks.
Linding, R. and Jensen, L.J. and Pasculescu, A. and Olhovsky, M. and Colwill, K. and Bork, P. and Yaffe, M.B. and Pawson, T.
Nucleic Acids Research 36 (Database issue): D695-D699. January 2008

2007

MeCP2 interacts with HP1 and modulates its heterochromatin association during myogenic differentiation.
Agarwal, N. and Hardt, T. and Brero, A. and Nowak, D. and Rothbauer, U. and Becker, A. and Leonhardt, H. and Cardoso, M.C.
Nucleic Acids Research 35 (16): 5402-5408. August 2007

Update of the G2D tool for prioritization of gene candidates to inherited diseases.
Perez-Iratxeta, C. and Bork, P. and Andrade-Navarro, M.A.
Nucleic Acids Research 35 (Web Server Issue): W212-W216. July 2007

Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation.
Schermelleh, L. and Haemmer, A. and Spada, F. and Roesing, N. and Meilinger, D. and Rothbauer, U. and Cardoso, C.M. and Leonhardt, H.
Nucleic Acids Research 35 (13): 4301-4312. July 2007

3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.
Via, A. and Peluso, D. and Gherardini, P.F. and Rinaldis, E.D. and Colombo, T. and Ausiello, G. and Helmer-Citterich, M.
Nucleic Acids Research 35 (Web Server Issue): W416-W419. July 2007

Conditional brain-specific knockdown of MAPK using Cre/loxP regulated RNA interference.
Hitz, C. and Wurst, W. and Kuehn, R.
Nucleic Acids Research 35 (12): e90. June 2007

Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach.
Morgan, H.P. and Estibeiro, P. and Wear, M.A. and Max, K.E. and Heinemann, U. and Cubeddu, L. and Gallagher, M.P. and Sadler, P.J. and Walkinshaw, M.D.
Nucleic Acids Research 35 (10): e75. May 2007

Vectors for co-expression of an unrestricted number of proteins.
Scheich, C. and Kuemmel, D. and Soumailakakis, D. and Heinemann, U. and Buessow, K.
Nucleic Acids Research 35 (6): e43. March 2007

Development of a species-specific RNA polymerase I-based shRNA expression vector.
Brenz Verca, M.S. and Weber, P. and Mayer, C. and Graf, C. and Refojo, D. and Kuehn, R. and Grummt, I. and Lutz, B.
Nucleic Acids Research 35 (2): e10. January 2007

UniHI: an entry gate to the human protein interactome.
Chaurasia, G. and Iqbal, Y. and Haenig, C. and Herzel, H. and Wanker, E.E. and Futschik, M.E.
Nucleic Acids Research 35 (Database Issue): D590-D594. January 2007

Developments in CORG: a gene-centric comparative genomics resource.
Dieterich, C. and Franz, M.W. and Vingron, M.
Nucleic Acids Research 35 (Database issue): D32-D35. January 2007

Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus.
Dieterich, C. and Roeseler, W. and Sobetzko, P. and Sommer, R.J.
Nucleic Acids Research 35 (Database issue): D498-D502. January 2007

New developments in the InterPro database.
Mulder, N.J. and Apweiler, R. and Attwood, T.K. and Bairoch, A. and Bateman, A. and Binns, D. and Bork, P. and Buillard, V. and Cerutti, L. and Copley, R. and Courcelle, E. and Das, U. and Daugherty, L. and Dibley, M. and Finn, R. and Fleischmann, W. and Gough, J. and Haft, D. and Hulo, N. and Hunter, S. and Kahn, D. and Kanapin, A. and Kejariwal, A. and Labarga, A. and Langendijk-Genevaux, P.S. and Lonsdale, D. and Lopez, R. and Letunic, I. and Madera, M. and Maslen, J. and McAnulla, C. and McDowall, J. and Mistry, J. and Mitchell, A. and Nikolskaya, A.N. and Orchard, S. and Orengo, C. and Petryszak, R. and Selengut, J.D. and Sigrist, C.J. and Thomas, P.D. and Valentin, F. and Wilson, D. and Wu, C.H. and Yeats, C.
Nucleic Acids Research 35 (Database Issue): D224-D228. January 2007

STRING 7 - recent developments in the integration and prediction of protein interactions.
von Mering, C. and Jensen, L.J. and Kuhn, M. and Chaffron, S. and Doerks, T. and Krueger, B. and Snel, B. and Bork, P.
Nucleic Acids Research 35 (Database Issue): D358-D362. January 2007

2006

Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction.
Ohler, U.
Nucleic Acids Research 34 (20): 5943-5950. November 2006

Differential recruitment of DNA Ligase I and III to DNA repair sites.
Mortusewicz, O. and Rothbauer, U. and Cardoso, M.C. and Leonhardt, H.
Nucleic Acids Research 34 (12): 3523-3532. 19 July 2006

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
Suyama, M. and Torrents, D. and Bork, P.
Nucleic Acids Research 34 (Web Server Issue): W609-W612. 1 July 2006

A translation control reporter system (TCRS) for the analysis of translationally controlled processes in the vertebrate cell.
Wiesenthal, V. and Leutz, A. and Calkhoven, C.F.
Nucleic Acids Research 34 (3): e23. 10 February 2006

SMART 5: domains in the context of genomes and networks.
Letunic, I. and Copley, R.R. and Pils, B. and Pinkert, S. and Schultz, J. and Bork, P.
Nucleic Acids Research 34 (Database Issue): D257-D260. 1 January 2006

Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution.
Zeeb, M. and Max, K.E.A. and Weininger, U. and Loew, C. and Sticht, H. and Balbach, J.
Nucleic Acids Research 34 (16): 4561-4571. 2006

2005

Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations.
Rohs, R. and Bloch, I. and Sklenar, H. and Shakked, Z.
Nucleic Acids Research 33 (22): 7048-7057. 13 December 2005

Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs.
Meyer, I.M. and Miklos, I.
Nucleic Acids Research 33 (19): 6338-6348. 7 November 2005

PCNA acts as a stationary loading platform for transiently interacting Okazaki fragment maturation proteins.
Sporbert, A. and Domaing, P. and Leonhardt, H. and Cardoso, M.C.
Nucleic Acids Research 33 (11): 3521-3528. 21 June 2005

Single copy shRNA configuration for ubiquitous gene knockdown in mice.
Seibler, J. and Kueter-Luks, B. and Kern, H. and Streu, S. and Plum, L. and Mauer, J. and Kuehn, R. and Bruening, J.C. and Schwenk, F.
Nucleic Acids Research 33 (7): e67. 14 April 2005

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.
Zdobnov, E.M. and Campillos, M. and Harrington, E.D. and Torrents, D. and Bork, P.
Nucleic Acids Research 33 (3): 946-954. 16 February 2005

InterPro, progress and status in 2005.
Mulder, N.J. and Apweiler, R. and Attwood, T.K. and Bairoch, A. and Bateman, A. and Binns, D. and Bradley, P. and Bork, P. and Bucher, P. and Cerutti, L. and Copley, R. and Courcelle, E. and Das, U. and Durbin, R. and Fleischmann, W. and Gough, J. and Haft, D. and Harte, N. and Hulo, N. and Kahn, D. and Kanapin, A. and Krestyaninova, M. and Lonsdale, D. and Lopez, R. and Letunic, I. and Madera, M. and Maslen, J. and McDowall, J. and Mitchell, A. and Nikolskaya, A.N. and Orchard, S. and Pagni, M. and Ponting, C.P. and Quevillon, E. and Selengut, J. and Sigrist, C.J. and Silventoinen, V. and Studholme, D.J. and Vaughan, R. and Wu, C.H.
Nucleic Acids Research 33 (Database Issue): D201-D205. 1 January 2005

STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
von Mering, C. and Jensen, L.J. and Snel, B. and Hooper, S.D. and Krupp, M. and Foglierini, M. and Jouffre, N. and Huynen, M.A. and Bork, P.
Nucleic Acids Research 33 (Database Issue): D433-D437. 1 January 2005

2004

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.
Doerks, T. and von Mering, C. and Bork, P.
Nucleic Acids Research 32 (21): 6321-6326. 1 December 2004

A comparative method for finding and folding RNA secondary structures within protein-coding regions.
Pedersen, J.S. and Meyer, I.M. and Forsberg, R. and Simmonds, P. and Hein, J.
Nucleic Acids Research 32 (16): 4925-4936. 24 September 2004

Riboswitch finder - a tool for identification of riboswitch RNAs.
Bengert, P. and Dandekar, T.
Nucleic Acids Research 32 (Web Server Issue): W154-W159. 1 July 2004

ArrayProspector: a web resource of functional associations inferred from microarray expression data.
Jensen, L.J. and Lagarde, J. and von Mering, C. and Bork, P.
Nucleic Acids Research 32 (Web Server Issue): W445-W448. 1 July 2004

Recognition of DNA by omega protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: analysis of binding to operator DNA with one to four heptad repeats.
de la Hoz, A.B. and Pratto, F. and Misselwitz, R. and Speck, C. and Weihofen, W. and Welfle, K. and Saenger, W. and Welfle, H. and Alonso, J.C.
Nucleic Acids Research 32 (10): 3136-3147. 9 June 2004

Gene structure conservation aids similarity based gene prediction.
Meyer, I.M. and Durbin, R.
Nucleic Acids Research 32 (2): 776-783. 4 February 2004

SMART 4.0: towards genomic data integration.
Letunic, I. and Copley, R.R. and Schmidt, S. and Ciccarelli, F.D. and Doerks, T. and Schultz, J. and Ponting, C.P. and Bork, P.
Nucleic Acids Research 32 (Database Issue): D142-D144. 1 January 2004

EASED: Extended alternatively spliced EST database.
Pospisil, H. and Herrmann, A. and Bortfeldt, R.H. and Reich, J.
Nucleic Acids Research 32 (Database Issue): D70-D74. 1 January 2004

2003

The Frog Prince: a reconstructed transposon from Rana pipiens with high transpositional activity in vertebrate cells.
Miskey, C. and Izsvak, Z. and Plasterk, R.H. and Ivics, Z.
Nucleic Acids Research 31 (23): 6873-6881. 1 December 2003

A software tool-box for analysis of regulatory RNA elements.
Bengert, P. and Dandekar, T.
Nucleic Acids Research 31 (13): 3441-3445. 1 July 2003

Update on XplorMed: a web server for exploring scientific literature.
Perez-Iratxeta, C. and Perez, A.J. and Bork, P. and Andrade-Navarro, M.A.
Nucleic Acids Research 31 (13): 3866-3868. 1 July 2003

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins.
Puntervoll, P. and Linding, R. and Gemund, C. and Chabanis-Davidson, S. and Mattingsdal, M. and Cameron, S. and Martin, D.M.A. and Ausiello, G. and Brannetti, B. and Costantini, A. and Ferre, F. and Maselli, V. and Via, A. and Cesareni, G. and Diella, F. and Superti-Furga, G. and Wyrwicz, L. and Ramu, C. and McGuigan, C. and Gudavalli, R. and Letunic, I. and Bork, P. and Rychlewski, L. and Kuester, B. and Helmer-Citterich, M. and Hunter, W.N. and Aasland, R. and Gibson, T.J.
Nucleic Acids Research 31 (13): 3625-3630. 1 July 2003

The nicking homing endonuclease I-BasI is encoded by a group I intron in the DNA polymerase gene of the Bacillus thuringiensis phage Bastille.
Landthaler, M. and Shub, D.A.
Nucleic Acids Research 31 (12): 3071-3077. 15 June 2003

The DNA-bending protein HMGB1 is a cellular cofactor of Sleeping Beauty transposition.
Zayed, H. and Izsvak, Z. and Khare, D. and Heinemann, U. and Ivics, Z.
Nucleic Acids Research 31 (9): 2313-2322. 1 May 2003

Rapid generation of inducible mouse mutants.
Seibler, J. and Zevnik, B. and Kueter-Luks, B. and Andreas, S. and Kern, H. and Hennek, T. and Rode, A. and Heimann, C. and Faust, N. and Kauselmann, G. and Schoor, M. and Jaenisch, R. and Rajewsky, K. and Kuehn, R. and Schwenk, F.
Nucleic Acids Research 31 (4): e12. 15 February 2003

The InterPro Database, 2003 brings increased coverage and new features.
Mulder, N.J. and Apweiler, R. and Attwood, T.K. and Bairoch, A. and Barrell, D. and Bateman, A. and Binns, D. and Biswas, M. and Bradley, P. and Bork, P. and Bucher, P. and Copley, R.R. and Courcelle, E. and Das, U. and Durbin, R. and Falquet, L. and Fleischmann, W. and Griffiths-Jones, S. and Haft, D. and Harte, N. and Hulo, N. and Kahn, D. and Kanapin, A. and Krestyaninova, M. and Lopez, R. and Letunic, I. and Lonsdale, D. and Silventoinen, V. and Orchard, S.E. and Pagni, M. and Peyruc, D. and Ponting, C.P. and Selengut, J.D. and Servant, F. and Sigrist, C.J.A. and Vaughan, R. and Zdobnov, E.M.
Nucleic Acids Research 31 (1): 315-318. 1 January 2003

STRING: a database of predicted functional associations between proteins.
von Mering, C. and Huynen, M. and Jaeggi, D. and Schmidt, S. and Bork, P. and Snel, B.
Nucleic Acids Research 31 (1): 258-261. 1 January 2003

CORG: a database for COmparative Regulatory Genomics.
Dieterich, C. and Wang, H. and Rateitschak, K. and Luz, H. and Vingron, M.
Nucleic Acids Research 31 (1): 55-57. 2003

2002

High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.
Werner, E. and Wende, W. and Pingoud, A. and Heinemann, U.
Nucleic Acids Research 30 (18): 3962-3971. 15 September 2002

Human non-synonymous SNPs: server and survey.
Ramensky, V. and Bork, P. and Sunyaev, S.
Nucleic Acids Research 30 (17): 3894-3900. 1 September 2002

Counting CAG repeats in the Huntington's disease gene by restriction endonuclease EcoP15I cleavage.
Moencke-Buchner, E. and Reich, S. and Muecke, M. and Reuter, M. and Messer, W. and Wanker, E.E. and Krueger, D.H.
Nucleic Acids Research 30 (16): e83. 15 August 2002

Enhanced efficiency through nuclear localization signal fusion on phage PhiC31-integrase: activity comparison with Cre and FLPe recombinase in mammalian cells.
Andreas, S. and Schwenk, F. and Kueter-Luks, B. and Faust, N. and Kuehn, R.
Nucleic Acids Research 30 (11): 2299-2306. 1 June 2002

CopR binds and bends its target DNA: a footprinting and fluorescence resonance energy transfer study.
Steinmetzer, K. and Behlke, J. and Brantl, S. and Lorenz, M.
Nucleic Acids Research 30 (9): 2052-2060. 1 May 2002

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
Fredman, D. and Siegfried, M. and Yuan, Y.P. and Bork, P. and Lehvaslaiho, H. and Brookes, A.J.
Nucleic Acids Research 30 (1): 387-391. 1 January 2002

Recent improvements to the SMART domain-based sequence annotation resource.
Letunic, I. and Goodstadt, L. and Dickens, N.J. and Doerks, T. and Schultz, J. and Mott, R. and Ciccarelli, F. and Copley, R.R. and Ponting, C.P. and Bork, P.
Nucleic Acids Research 30 (1): 242-244. 1 January 2002

Two self-splicing group I introns in the ribonucleotide reductase large subunit gene of Staphylococcus aureus phage Twort.
Landthaler, M. and Begley, U. and Lau, N.C. and Shub, D.A.
Nucleic Acids Research 30 (9): 1935-1943. 2002

2000

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
Snel, B. and Lehmann, G. and Bork, P. and Huynen, M.A.
Nucleic Acids Research 28 (18): 3442-3444. 15 September 2000

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
Dandekar, T. and Huynen, M.A. and Regula, J. and Ueberle, B. and Zimmermann, C.U. and Andrade, M.A. and Doerks, T. and Sanches-Pulido, L. and Snel, B. and Suyama, M. and Yuan, Y.P. and Herrmann, R. and Bork, P.
Nucleic Acids Research 28 (17): 3278-3288. 1 September 2000

Retrotransposition of the vertical bar factor, a non-long terminal repeat retrotransposon of Drosophila, generates tandem repeats at the 3' end.
Chaboissier, M.C. and Finnegan, D. and Bucheton, A.
Nucleic Acids Research 28 (13): 2467-2472. 1 July 2000

HGBASE: a database of SNPs and other variations in and around human genes.
Brookes, A.J. and Lehvaslaiho, H. and Siegfried, M. and Boehm, J.G. and Yuan, Y.P. and Sarkar, C.M. and Bork, P. and Ortigao, F.
Nucleic Acids Research 28 (1): 356-360. 1 January 2000

SMART: a web-based tool for the study of genetically mobile domains.
Schultz, J. and Copley, R.R. and Doerks, T. and Ponting, C.P. and Bork, P.
Nucleic Acids Research 28 (1): 231-234. 1 January 2000

1999

Telomerase protein rather than its RNA is the target of phosphorothioate-modified oligonucleotides.
Matthes, E. and Lehmann, C.
Nucleic Acids Research 27 (4): 1152-1158. 15 February 1999

SMART: identification and annotation of domains from signalling and extracellular protein sequences.
Ponting, C.P. and Schultz, J. and Milpetz, F. and Bork, P.
Nucleic Acids Research 27 (1): 229-232. 1 January 1999

1998

Automatic detection of conserved RNA structure elements in complete RNA virus genomes.
Hofacker, I.L. and Fekete, M. and Flamm, C. and Huynen, M.A. and Rauscher, S. and Stolorz, P.E. and Stadler, P.F.
Nucleic Acids Research 26 (16): 3825-3836. 15 August 1998

Characterization of protein-binding to the spinach chloroplast psbA mRNA 5' untranslated region.
Alexander, C. and Faber, N. and Klaff, P.
Nucleic Acids Research 26 (10): 2265-2272. 15 May 1998

Signal-dependent degradation of IkappaBalpha is mediated by an inducible destruction box that can be transferred to NF-kappaB, bcl-3 or p53.
Wulczyn, F.G. and Krappmann, D. and Scheidereit, C.
Nucleic Acids Research 26 (7): 1724-1730. 1 April 1998

Temporally and spatially regulated somatic mutagenesis in mice.
Schwenk, F. and Kuehn, R. and Angrand, P.O. and Rajewsky, K. and Stewart, A.F.
Nucleic Acids Research 26 (6): 1427-1432. 15 March 1998

LDLR Database (second edition): new additions to the database and the software, and results of the first molecular analysis.
Varret, M. and Rabes, J.P. and Thiart, R. and Kotze, M.J. and Baron, H. and Cenarro, A. and Descamps, O. and Ebhardt, M. and Hondelijn, J.C. and Kostner, G.M. and Miyake, Y. and Pocovi, M. and Schmidt, H. and Schuster, H. and Stuhrmann, M. and Yamamura, T. and Junien, C. and Beroud, C. and Boileau, C.
Nucleic Acids Research 26 (1): 248-252. 1 January 1998

1997

Efficient transcription of an immunoglobulin kappa promoter requires specific sequence elements overlapping with and downstream of the transcriptional start site.
Pelletier, M.R. and Hatada, E.N. and Scholz, G. and Scheidereit, C.
Nucleic Acids Research 25 (20): 3995-4003. 15 October 1997

Tetracycline-controlled transcription in eukaryotes: novel transactivators with graded transactivation potential.
Baron, U. and Gossen, M. and Bujard, H.
Nucleic Acids Research 25 (14): 2723-2729. 15 July 1997

Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins.
Boehm, S. and Frishman, D. and Mewes, H.
Nucleic Acids Research 25 (12): 2464-2469. 15 June 1997

Cre-mediated somatic site-specific recombination in mice.
Akagi, K. and Sandig, V. and Vooijs, M. and van der Valk, M. and Giovannini, M. and Strauss, M. and Berns, A.
Nucleic Acids Research 25 (9): 1766-1773. 1 May 1997

Hairpin-dimer equilibrium of a parallel-stranded DNA hairpin: formation of a four-stranded complex.
Dornberger, U. and Behlke, J. and Birch-Hirschfeld, E. and Fritzsche, H.
Nucleic Acids Research 25 (4): 822-829. 15 February 1997

1995

Species- and tissue-specific expression of the C-terminal alternatively spliced form of the tumor suppressor p53.
Will, K. and Warnecke, G. and Bergman, S. and Deppert, W.
Nucleic Acids Research 23 (20): 4023-4028. 25 October 1995

Co-regulation of two gene activities by tetracycline via a bidirectional promoter.
Baron, U. and Freundlieb, S. and Gossen, M. and Bujard, H.
Nucleic Acids Research 23 (17): 3605-3606. 11 September 1995

The processing of macronuclear-destined DNA sequences microinjected into the macronuclear anlagen of the hypotrichous ciliate Stylonchia lemnae.
Wen, J.P. and Eder, C. and Lipps, H.J.
Nucleic Acids Research 23 (10): 1704-1709. 25 May 1995

1994

A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?
Koonin, E. and Bork, P. and Sander, C.
Nucleic Acids Research 22 (11): 2166-2167. 11 June 1994

1993

A method for the generation of YAC transgenic mice by pronuclear microinjection.
Schedl, A. and Larin, Z. and Montoliu, L. and Thies, E. and Kelsey, G. and Lehrach, H. and Schuetz, G.
Nucleic Acids Research 21 (20): 4783-4787. 11 October 1993

Identification of differentially expressed mRNA species by an improved display technique (DDRT-PCR).
Bauer, D. and Mueller, H. and Reich, J. and Riedel, H. and Ahrenkiel, V. and Warthoe, P. and Strauss, M.
Nucleic Acids Research 21 (18): 4272-4280. 11 September 1993

Anhydrotetracycline, a novel effector for tetracycline controlled gene expression systems in eukaryotic cells.
Gossen, M. and Bujard, H.
Nucleic Acids Research 21 (18): 4411-4412. 11 September 1993

Rapid method of total RNA mini-preparation from eucaryotic cells.
Walther, W. and Stein, U. and Uckert, W.
Nucleic Acids Research 21 (7): 1682. 11 April 1993

An expanding family of helicases within the "DEAD/H" superfamily.
Bork, P. and Koonin, E.
Nucleic Acids Research 21 (3): 751-752. 11 February 1993

Conformation of d (GGGATCCC) 2 in crystals and in solution studied by X-ray diffraction, Raman spectroscopy and molecular modelling.
Fabian, H. and Hoelzer, W. and Heinemann, U. and Sklenar, H. and Welfle, H.
Nucleic Acids Research 21 (3): 569-576. 11 February 1993

1992

Structure of the phenylalanyl-tRNA synthetase genes from Thermus thermophilus HB8 and their expression in Escherichia coli.
Kreutzer, R. and Kruft, V. and Bobkova, E.V. and Lavrik, O.I. and Sprinzl, M.
Nucleic Acids Research 20 (16): 4173-4178. 25 August 1992

Ssp5230I, a novel isoschizomer of AatII from Streptomyces recognizing 5'-GACGT/C-3'.
Knoblich, I.M. and Sellmann, E. and Kaluza, K. and Frey, B. and Auer, J. and Schmitz, G.G. and Westermann, P.
Nucleic Acids Research 20 (9): 2378. 11 May 1992

Bsp423I, a novel isoschizomer of BbvI from Bacillus recognizing 5'-GCAGC-3'.
Sellmann, E. and Knoblich, I.M. and Kaluza, K. and Frey, B. and Schmitz, G.G. and Westermann, P.
Nucleic Acids Research 20 (9): 2377. 11 May 1992

KorB protein of promiscuous plasmid RP4 recognizes inverted sequence repetitions in regions essential for conjugative plasmid transfer.
Balzer, D. and Ziegelin, G. and Pansegrau, W. and Kruft, W. and Lanka, E.
Nucleic Acids Research 20 (8): 1851-1858. 25 April 1992

Tissue restricted expression and chromosomal localization of the YB-1 gene encoding a 42 kD nuclear CCAAT binding protein.
Spitkovsky, D.D. and Royer-Pokora, B. and Delius, H. and Kisseljov, F. and Jenkins, N.A. and Gilbert, D.J. and Copeland, N.G. and Royer, H.D.
Nucleic Acids Research 20 (4): 797-803. 25 February 1992

1991

Non-leucine residues in the leucine repeats of Fos and Jun contribute to the stability and determine the specificity of dimerization.
Schuermann, M. and Hunter, J.B. and Hennig, M. and Mueller, R.
Nucleic Acids Research 19 (4): 739-746. 25 February 1991

This list was generated on Wed Dec 12 02:33:01 2018 CET.
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