Browse by Journal Title

2024

iSuRe-HadCre is an essential tool for effective conditional genetics.
Garcia-Gonzalez, I., Rocha, S.F., Hamidi, A., Garcia-Ortega, L., Regano, A., Sanchez-Muñoz, M.S., Lytvyn, M., Garcia-Cabero, A., Roig-Soucase, S., Schoofs, H., Castro, M., Sabata, H., Potente, M., Graupera, M., Makinen, T. and Benedito, R.
Nucleic Acids Research 52 (13): e56. 22 July 2024

Liam tackles complex multimodal single-cell data integration challenges.
Rautenstrauch, P. and Ohler, U.
Nucleic Acids Research 52 (12): e52. 8 July 2024

REEV: review, evaluate and explain variants.
Hramyka, D., Sczakiel, H.L., Zhao, M.X., Stolpe, O., Nieminen, M., Adam, R., Danyel, M., Einicke, L., Hägerling, R., Knaus, A., Mundlos, S., Schwartzmann, S., Seelow, D., Ehmke, N., Mensah, M.A., Boschann, F., Beule, D. and Holtgrewe, M.
Nucleic Acids Research 52 (W1): W148-W158. 5 July 2024

Despite the odds: formation of the SARS-CoV-2 methylation complex.
Matsuda, A., Plewka, J., Rawski, M., Mourão, A., Zajko, W., Siebenmorgen, T., Kresik, L., Lis, K., Jones, A.N., 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., Pyrć, K. and Czarna, A.
Nucleic Acids Research 52 (11): 6441-6458. 24 June 2024

Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation.
Roske, Y., Cappel, C., Cremer, N., Hoffmann, P., Koudelka, T., Tholey, A., Heinemann, U., Daumke, O. and Damme, M.
Nucleic Acids Research 52 (1): 370-384. 11 January 2024

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
Schmidt, T.S.B., Fullam, A., Ferretti, P., Orakov, A., Maistrenko, O.M., Ruscheweyh, H.J., Letunic, I., Duan, Y., Van Rossum, T., Sunagawa, S., Mende, D.R., Finn, R.D., Kuhn, M., Pedro Coelho, L. and Bork, P.
Nucleic Acids Research 52 (D1): D777-D783. 5 January 2024

2023

e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.
Tsybulskyi, V., Semenchenko, E. and Meyer, I.M.
Nucleic Acids Research 51 (W1): W160-W167. 5 July 2023

Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart.
Milenkovic, I., Santos Vieira, H.G., Lucas, M.C., Ruiz-Orera, J., Patone, G., Kesteven, S., Wu, J., Feneley, M., Espadas, G., Sabidó, E., Hübner, N., van Heesch, S., Völkers, M. and Novoa, E.M.
Nucleic Acids Research 51 (11): 5301-5324. 23 June 2023

CYCLeR - a novel tool for the full isoform assembly and quantification of circRNAs.
Stefanov, S.R. and Meyer, I.M.
Nucleic Acids Research 51 (2): e10. 25 January 2023

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Fullam, A., Letunic, I., Schmidt, T.S.B., Ducarmon, Q.R., Karcher, N., Khedkar, S., Kuhn, M., Larralde, M., Maistrenko, O.M., Malfertheiner, L., Milanese, A., Rodrigues, J.F.M., Sanchis-López, C., Schudoma, C., Szklarczyk, D., Sunagawa, S., Zeller, G., Huerta-Cepas, J., von Mering, C., Bork, P. and Mende, D.R.
Nucleic Acids Research 51 (D1): D760-D766. 6 January 2023

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A.L., Fang, T., Doncheva, N.T., Pyysalo, S., Bork, P., Jensen, L.J. and von Mering, C.
Nucleic Acids Research 51 (D1): D638-D646. 6 January 2023

CORUM: the comprehensive resource of mammalian protein complexes-2022.
Tsitsiridis, G., Steinkamp, R., Giurgiu, M., Brauner, B., Fobo, G., Frishman, G., Montrone, C. and Ruepp, A.
Nucleic Acids Research 51 (D1): D539-D545. 6 January 2023

2022

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA.
Keil, P., Wulf, A., Kachariya, N., Reuscher, S., Hühn, K., Silbern, I., Altmüller, J., Keller, M., Stehle, R., Zarnack, K., Sattler, M., Urlaub, H. and Sträßer, K.
Nucleic Acids Research : gkac1206. 30 December 2022

Cluster-independent marker feature identification from single-cell omics data using SEMITONES.
Vlot, A.H.C., Maghsudi, S. and Ohler, U.
Nucleic Acids Research 50 (18): e107. 14 October 2022

ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence.
Tsybulskyi, V. and Meyer, I.M.
Nucleic Acids Research 50 (15): e85. 26 August 2022

Exon junction complex-associated multi-adapter RNPS1 nucleates splicing regulatory complexes to maintain transcriptome surveillance.
Schlautmann, L.P., Lackmann, J.W., Altmüller, J., Dieterich, C., Boehm, V. and Gehring, N.H.
Nucleic Acids Research 50 (10): 5899-5918. 10 June 2022

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.
Khedkar, S., Smyshlyaev, G., Letunic, I., Maistrenko, O.M., Coelho, L.P., Orakov, A., Forslund, S.K., Hildebrand, F., Luetge, M., Schmidt, T.S.B., Barabas, O. and Bork, P.
Nucleic Acids Research 50 (6): 3155-3168. 8 April 2022

2021

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.
Glaser, L.V., Steiger, M., Fuchs, A., van Bömmel, A., Einfeldt, E., Chung, H.R., Vingron, M. and Meijsing, S.H.
Nucleic Acids Research 49 (21): 12178-12195. 2 December 2021

Charcot-Marie-Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response.
Mendonsa, S., von Kuegelgen, N., Bujanic, L. and Chekulaeva, M.
Nucleic Acids Research 49 (17): 10007-10017. 27 September 2021

PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases.
Garg, A., Roske, Y., Yamada, S., Uehata, T., Takeuchi, O. and Heinemann, U.
Nucleic Acids Research 49 (9): 5369-5381. 21 May 2021

Systematic identification of A-to-I RNA editing in zebrafish development and adult organs.
Buchumenski, I., Holler, K., Appelbaum, L., Eisenberg, E., Junker, J.P. and Levanon, E.Y.
Nucleic Acids Research 49 (8): 4325-4337. 7 May 2021

DDX3 depletion represses translation of mRNAs with complex 5' UTRs.
Calviello, L., Venkataramanan, S., Rogowski, K.J., Wyler, E., Wilkins, K., Tejura, M., Thai, B., Krol, J., Filipowicz, W., Landthaler, M. and Floor, S.N.
Nucleic Acids Research 49 (9): 5336-5350. May 2021

The CONJUDOR pipeline for multiplexed knockdown of gene pairs identifies RBBP-5 as a germ cell reprogramming barrier in C. elegans.
Kazmierczak, M., Farré i Díaz, C., Ofenbauer, A., Herzog, S. and Tursun, B.
Nucleic Acids Research 49 (4): e22. 26 February 2021

CoBold: a method for identifying different functional classes of transient RNA structure features that can impact RNA structure formation in vivo.
Martín, A.L., Mounir, M. and Meyer, I.M.
Nucleic Acids Research 49 (4): e19. 26 February 2021

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.
Gurumayum, S., Jiang, P., Hao, X., Campos, T.L., Young, N.D., Korhonen, P.K., Gasser, R.B., Bork, P., Zhao, X.M., He, L.J. and Chen, W.H.
Nucleic Acids Research 49 (D1): D998-D1003. 8 January 2021

SMART: recent updates, new developments and status in 2020.
Letunic, I., Khedkar, S. and Bork, P.
Nucleic Acids Research 49 (D1): D458-D460. 8 January 2021

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Szklarczyk, D., Gable, A.L., Nastou, K.C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N.T., Legeay, M., Fang, T., Bork, P., Jensen, L.J. and von Mering, C.
Nucleic Acids Research 49 (D): D605-D612. 8 January 2021

2020

Comprehensive analysis of translation from overexpressed circular RNAs reveals pervasive translation from linear transcripts.
Ho-Xuan, H., Glažar, P., Latini, C., Heizler, K., Haase, J., Hett, R., Anders, M., Weichmann, F., Bruckmann, A., Van den Berg, D., Hüttelmaier, S., Rajewsky, N., Hackl, C. and Meister, G.
Nucleic Acids Research 48 (18): 10368-10382. 9 October 2020

R-chie: a web server and R package for visualizing cis and trans RNA-RNA, RNA-DNA and DNA-DNA interactions.
Tsybulskyi, V., Mounir, M. and Meyer, I.M.
Nucleic Acids Research 48 (18): e105. 9 October 2020

CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex.
Gerbracht, J.V., Boehm, V., Britto-Borges, T., Kallabis, S., Wiederstein, J.L., Ciriello, S., Aschemeier, D.U., Krüger, M., Frese, C.K., Altmüller, J., Dieterich, C. and Gehring, N.H.
Nucleic Acids Research 48 (15): 8626-8644. 4 September 2020

VarFish: comprehensive DNA variant analysis for diagnostics and research.
Holtgrewe, M., Stolpe, O., Nieminen, M., Mundlos, S., Knaus, A., Kornak, U., Seelow, D., Segebrecht, L., Spielmann, M., Fischer-Zirnsak, B., Boschann, F., Scholl, U., Ehmke, N. and Beule, D.
Nucleic Acids Research 48 (W1): W162-W169. 2 July 2020

SuperCYPsPred - a web server for the prediction of cytochrome activity.
Banerjee, P., Dunkel, M., Kemmler, E. and Preissner, R.
Nucleic Acids Research 48 (W1): W580-W585. July 2020

FAM46B is a prokaryotic-like cytoplasmic poly(A) polymerase essential in human embryonic stem cells.
Hu, J.L., Liang, H., Zhang, H., Yang, M.Z., Sun, W., Zhang, P., Luo, L., Feng, J.X., Bai, H., Liu, F., Zhang, T., Yang, J.Y., Gao, Q., Long, Y., Ma, X.Y., Chen, Y., Zhong, Q., Yu, B., Liao, S., Wang, Y., Zhao, Y., Zeng, M.S., Cao, N., Wang, J., Chen, W., Yang, H.T. and Gao, S.
Nucleic Acids Research 48 (5): 2733-2748. 18 March 2020

The human ZC3H3 and RBM26/27 proteins are critical for PAXT-mediated nuclear RNA decay.
Silla, T., Schmid, M., Dou, Y., Garland, W., Milek, M., Imami, K., Johnsen, D., Polak, P., Andersen, J.S., Selbach, M., Landthaler, M. and Jensen, T.
Nucleic Acids Research 48 (5): 2518-2530. 18 March 2020

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Mende, D.R., Letunic, I., Maistrenko, O.M., Schmidt, T.S.B., Milanese, A., Paoli, L., Hernández-Plaza, A., Orakov, A.N., Forslund, S.K., Sunagawa, S., Zeller, G., Huerta-Cepas, J., Coelho, L.P. and Bork, P.
Nucleic Acids Research 48 (D1): D621-D625. 8 January 2020

A single amino acid switch converts the sleeping beauty transposase into an efficient unidirectional excisionase with utility in stem cell reprogramming.
Kesselring, L., Miskey, C., Zuliani, C., Querques, I., Kapitonov, V., Laukó, A., Fehér, A., Palazzo, A., Diem, T., Lustig, J., Sebe, A., Wang, Y., Dinnyés, A., Izsvák, Z., Barabas, O. and Ivics, Z.
Nucleic Acids Research 48 (1): 316-331. 1 January 2020

2019

HOT or not: examining the basis of high-occupancy target regions.
Wreczycka, K., Franke, V., Uyar, B., Wurmus, R., Bulut, S., Tursun, B. and Akalin, A.
Nucleic Acids Research : gkz460. 20 June 2019

Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints.
Massip, F., Laurent, M., Brossas, C., Fernández-Justel, J.M., Gómez, M., Prioleau, M.N., Duret, L. and Picard, F.
Nucleic Acids Research 47 (10): 5114-5125. 4 June 2019

Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments.
Ciolli Mattioli, C., Rom, A., Franke, V., Imami, K., Arrey, G., Terne, M., Woehler, A., Akalin, A., Ulitsky, I. and Chekulaeva, M.
Nucleic Acids Research 47 (5): 2560-2573. 18 March 2019

Deciphering human ribonucleoprotein regulatory networks.
Mukherjee, N., Wessels, H.H., Lebedeva, S., Sajek, M., Ghanbari, M., Garzia, A., Munteanu, A., Yusuf, D., Farazi, T., Hoell, J.I., Akat, K.M., Akalin, A., Tuschl, T. and Ohler, U.
Nucleic Acids Research 47 (2): 570-581. 25 January 2019

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S.K., Cook, H., Mende, D.R., Letunic, I., Rattei, T., Jensen, L.J., von Mering, C. and Bork, P.
Nucleic Acids Research 47 (D1): D309-D314. 8 January 2019

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Szklarczyk, D., Gable, A.L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N.T., Morris, J.H., Bork, P., Jensen, L.J. and von Mering, C.
Nucleic Acids Research 47 (D1): D607-D613. 8 January 2019

2018

ProTox-II: a webserver for the prediction of toxicity of chemicals.
Banerjee, P., Eckert, A.O., 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., Frainay, C., Chazalviel, M., Cabanettes, F., Gloaguen, Y., Camenen, E., Merlet, B., Heux, S., Portais, J.C., Poupin, N., Vinson, F. and Jourdan, F.
Nucleic Acids Research 46 (W1): W495-W502. 2 July 2018

iPath3.0: interactive pathways explorer v3.
Darzi, Y., Letunic, I., 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., Nagy, G., Horvath, A., Czimmerer, Z., Cuaranta-Monroy, I., Poliska, S., Hays, T.T., Sauer, S., 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., Roske, Y., Schuetz, A., Walentin, K., Ibraimi, I., 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., Zhang, C., Zhang, Z., Hu, S., Lercher, M.J., Zhao, X.M., Bork, P., 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., Gohlke, B.O., Toguem, S.M.T., Preissner, S., 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., Eckert, O.A., Gohlke, B.O., Goede, A., Chen, Q., Devarakonda, P., Preissner, S. and Preissner, R.
Nucleic Acids Research 46 (D1): D1137-D1143. 4 January 2018

2017

Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities.
Bunina, D., Štefl, M., Huber, F., Khmelinskii, A., Meurer, M., Barry, J.D., Kats, I., Kirrmaier, D., Huber, W. and Knop, M.
Nucleic Acids Research 45 (19): 11144-11158. 2 November 2017

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.
Heller, D., Krestel, R., Ohler, U., 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., Fallmann, J., Yusuf, D., Will, S., Erxleben, A., Eggenhofer, F., Houwaart, T., Batut, B., Videm, P., Bagnacani, A., Wolfien, M., Lott, S.C., Hoogstrate, Y., Hess, W.R., Wolkenhauer, O., Hoffmann, S., Akalin, A., Ohler, U., 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., Kreuchwig, F., Tiemann, J.K.S., Kreuchwig, A., Ritschel, M., Kleinau, G., 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., Yusuf, D., Wurmus, R., Rajewsky, N., 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., Zharkov, D.O., Stahl, J., Gopanenko, Al.V., Tupikin, A.E., Kabilov, M.R., 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., Kirchner, M., Aharoni, R., Ciolli Mattioli, C., van den Bruck, D., Gutkovitch, N., Modepalli, V., Selbach, M., 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., Gasparoni, N., Gasparoni, G., Gianmoena, K., Cadenas, C., Polansky, J.K., Ebert, P., Nordstroem, K., Barann, M., Sinha, A., Froehler, S., Xiong, J., Dehghani Amirabad, A., Behjati Ardakani, F., Hutter, B., Zipprich, G., Felder, B., Eils, J., Brors, B., Chen, W., Hengstler, J.G., Hamann, A., Lengauer, T., Rosenstiel, P., 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., Pryputniewicz-Dobrinska, D., Nagy, E.E., Kaufman, C.D., Singh, M., Yant, S., Wang, J., Dalda, A., Kay, M.A., 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., Lu, G., Chen, X., 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., Letunic, I., Huerta-Cepas, J., Li, S.S., Forslund, K., 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., Morris, J.H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N.T., Roth, A., Bork, P., 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., Berber, B., 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., Prykhozhij, S.V., Schöne, S., Meierhofer, D., Sauer, S., 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., Rose, A.S., Tiemann, J.K.S., Goede, A., 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., Tamuri, A.U., Kultys, M., King, J., Godwin, J., Florescu, A.M., 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., Schlesinger, J., Schoenhals, S., Toenjes, M., Dunkel, I., Meierhofer, D., Cano, E., Schulz, K., Berger, M.F., Haack, T., Abdelilah-Seyfried, S., Bulyk, M.L., 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., van Noort, V., Lluch-Senar, M., Hennrich, M.L., Wodke, J.A.H., Yus, E., Alibes, A., Roma, G., Mende, D.R., Pesavento, C., Typas, A., Gavin, A.C., 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., Nickel, J., Otto, R., 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., 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. and Bork, P.
Nucleic Acids Research 44 (D1): D286-D293. 4 January 2016

The SIDER database of drugs and side effects.
Kuhn, M., Letunic, I., 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., Nickel, J., Omieczynski, C., Gohlke, B.O., 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., Santos, A., von Mering, C., Jensen, L.J., 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., Kühner, K., Kühn, R., Werfel, S., Engelhardt, S., 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., Anmarkrud, J.A., Kässens, J.C., Koch, S., Forster, M., Ellinghaus, E., Hov, J.R., Sauer, S., Schimmler, M., Ziemann, M., Görg, S., Jacob, F., Karlsen, T.H. and Franke, A.
Nucleic Acids Research 43 (11): e70. 23 June 2015

CWC22-dependent pre-mRNA splicing and eIF4A3 binding enables global deposition of exon junction complexes.
Steckelberg, A.L., Altmueller, J., Dieterich, C. and Gehring, N.H.
Nucleic Acids Research 43 (9): 4687-4700. 19 May 2015

Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum.
Staudacher, J.J., Naarmann-de Vries, I.S., Ujvari, S.J., Klinger, B., Kasim, M., Benko, E., Ostareck-Lederer, A., Ostareck, D.H., Bondke Persson, A., Lorenzen, S., Meier, J.C., Blüthgen, N., Persson, P.B., Henrion-Caude, A., 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., Erehman, J., Gohlke, B.O., Wilhelm, T., 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., Dieterich, C., Wurmus, R., Rajewsky, N., 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., Letunic, I., Parca, L., Garcia-Alonso, L., Dopazo, J., 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., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K.P., Kuhn, M., Bork, P., 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., Frank, C.L., Crawford, G.E. and Ohler, U.
Nucleic Acids Research 42 (19): 11865-11878. 29 October 2014

Single-cell RNA-seq: advances and future challenges.
Saliba, A.E., Westermann, A.J., Gorski, S.A. and Vogel, J.
Nucleic Acids Research 42 (14): 8845-8860. 18 August 2014

Alkemio: association of chemicals with biomedical topics by text and data mining.
Gijon-Correas, J.A., 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., 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., Reuter, S., 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., Dick, A., Woods, V.L., Liu, T., Li, S., Devignot, S., Weber, F., 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., Preissner, S.C., Nickel, J., Dunkel, M., 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., Szklarczyk, D., Pletscher-Frankild, S., Blicher, T.H., von Mering, C., 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., Nickel, J., Dunkel, M., 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., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldon, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, L.J., von Mering, C. and Bork, P.
Nucleic Acids Research 42 (1): D231-D239. 1 January 2014

CellFinder: a cell data repository.
Stachelscheid, H., Seltmann, S., Lekschas, F., Fontaine, J.F., Mah, N., Neves, M., Andrade-Navarro, M.A., 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., Barbosa-Silva, A., 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., Steif, A., 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., Oehme, I., Schroeder, C., Milde, T., Schier, M.C., Kopp-Schneider, A., Schulte, J.H., Fischer, M., De Preter, K., Pattyn, F., Castoldi, M., Muckenthaler, M.U., Kulozik, A.E., Westermann, F., 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., Minderjahn, J., Schmidl, C., Hoffmeister, H., Schmidhofer, S., Chen, W., Laengst, G., 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., Fischer, C., Kodelja, V., Behrens, S., Haas, S., Vingron, M., Timmermann, B., 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., You, X., Chen, T., Mackowiak, S.D., Friedlaender, M.R., Weigt, M., Du, H., Gogol-Doering, A., Chang, Z., Dieterich, C., 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., Wang, J., Sebe, A., Erdei, Z., Kajdi, R., Devaraj, A., Steinemann, D., Szuhai, K., Stein, U., Cantz, T., Schambach, A., Baum, C., Izsvák, Z., 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., Lippert, C., 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., Fontaine, J.F., Yildirimman, R., Raskó, T., Schaefer, M.H., Rasche, A., Porras, P., Vázquez-Álvarez, B.M., Russ, J., Rau, K., Foulle, R., Zenkner, M., Saar, K., Herwig, R., 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., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., 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., Letunic, I., 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., Dunkel, M., Gohlke, B.O., Preissner, S.C., Hoffmann, M.F., Bauer, J.M.J., Armstrong, J.D., Schaefer, M.H., Andrade-Navarro, M.A., Le Novere, N., Croning, M.D.R., Grant, S.G.N., van Nierop, P., 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., Gogol-Doering, A., Miskey, C., Chen, W., Cathomen, T., 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., Schütz, A., 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., Proctor, J.R., 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., 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., Hammani, K., Rojas, M., Voelker, R., Vargas-Suarez, M., 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., van Bemmel, J.G., Haase, S., Herce, H.D., Nowak, D., Meilinger, D., Stear, J.H., 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., Mackowiak, S.D., Li, N., 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., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T., Jensen, L.J., von Mering, C. and Bork, P.
Nucleic Acids Research 40 (D1): D284-D289. 1 January 2012

The Pfam protein families database.
Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E.L.L., Eddy, S.R., 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., Mackowiak, S.D., Jens, M., Maaskola, J., Kuntzagk, A., Rajewsky, N., Landthaler, M. and Dieterich, C.
Nucleic Acids Research 40 (1): D180-D186. January 2012

OGEE: an online gene essentiality database.
Chen, W.H., Minguez, P., 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., Szklarczyk, D., Franceschini, A., von Mering, C., 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., Karl, S., Baumann, B., Salles, D., Daniel, P., 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., Obermayer, B., Rajamani, S., 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., Schambach, A., Falk, C.S., Maetzig, T., Kuehle, J., Lange, K., Zychlinski, D., Heinz, N., Brugman, M.H., Goehring, G., Izsvak, Z., 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., Haase, S., Smeets, D., Schrode, N., Schmiedel, J.M., Bertulat, B., Herzel, H., 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., Hu, H.Y., Jiang, X., Maierhofer, V., Neb, E., He, L., Hu, Y., Hu, H., Li, N., 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., 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., Priller, F., 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., Mah, N., 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., Preissner, S., Dunkel, M., Worth, C.L., 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., Worth, C.L., Thaben, P., Matzig, C., Blasse, C., 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., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., 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., Harrington, E.D., Vinokourova, S., von Knebel Doeberitz, M., 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., 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., Wolf, C., Stribl, C., Javaheri, T., Schnuetgen, F., Ettinger, A., Ivics, Z., Hansen, J., Ruiz, P., von Melchner, H., 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., Chagin, V.O., Schermelleh, L., Martin, S., Pombo, A., Carlton, P.M., Gahl, A., Domaing, P., Birk, U., Leonhardt, H., Cremer, C. and Cardoso, M.C.
Nucleic Acids Research 38 (2): e8. March 2010

The Pfam protein families database.
Finn, R.D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J.E., Gavin, O.L., Gunasekaran, P., Ceric, G., Forslund, K., Holm, L., Sonnhammer, E.L.L., 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., Schmitt, T., Forslund, K., Köstler, T., Messina, D.N., Roopra, S., 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., Foerster, F., Keller, A., Schleicher, T., Ruderisch, B., Schwarz, R., Mueller, T., 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., Szklarczyk, D., Franceschini, A., Campillos, M., von Mering, C., Jensen, L.J., 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., Szklarczyk, D., Julien, P., Letunic, I., Roth, A., Kuhn, M., Powell, S., von Mering, C., Doerks, T., 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., Yuan, Y.P., Benner, A., Korff, S., 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., Seibel, P.N., Rahmann, S., Schoen, C., Huenerberg, M., Mueller-Reible, C., Dandekar, T., Karchin, R., Schultz, J. and Mueller, T.
Nucleic Acids Research 37 (18): 5959-5968. October 2009

MedlineRanker: flexible ranking of biomedical literature.
Fontaine, J.F., Barbosa-Silva, A., Schaefer, M., Huska, M.R., 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., 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., Mueller, J.J., 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., Gossen, M., Loew, R., Kentner, D., Berger, S., Goerlich, D., Bartsch, D., 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., Graifer, D., Malygin, A., Stahl, J., 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., Malhotra, S., Russ, J., Schnoegl, S., Haenig, C., 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., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Laugraud, A., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Mulder, N., Natale, D., Orengo, C., Quinn, A.F., Selengut, J.D., Sigrist, C.J., Thimma, M., Thomas, P.D., Valentin, F., Wilson, D., 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., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., 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., 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., Streitner, C., Meyer, I.M., 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., Kocman, I., Agrawal, V., Rahn, H.P., Besser, D. and Gossen, M.
Nucleic Acids Research 36 (17): e111. October 2008

KEGG Atlas mapping for global analysis of metabolic pathways.
Okuda, S., Yamada, T., Hamajima, M., Itoh, M., Katayama, T., Bork, P., 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., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.R., Ceric, G., Forslund, K., Eddy, S.R., 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., Kuhn, M., Dunkel, M., Campillos, M., Senger, C., Petsalaki, E., Ahmed, J., Urdiales, E.G., Gewiess, A., Jensen, L.J., Schneider, R., Skoblo, R., Russell, R.B., Bourne, P.E., 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., Berube, H., Letunic, I., Weeber, P.D., Gagneur, J., Girardot, C., Kapushesky, M., Arendt, D., Bork, P., Brazma, A., Furlong, E.E., 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., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. and Bork, P.
Nucleic Acids Research 36 (Database issue): D250-D254. January 2008

STITCH: interaction networks of chemicals and proteins.
Kuhn, M., von Mering, C., Campillos, M., 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., Jensen, L.J., Pasculescu, A., Olhovsky, M., Colwill, K., Bork, P., 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., Hardt, T., Brero, A., Nowak, D., Rothbauer, U., Becker, A., 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., 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., Haemmer, A., Spada, F., Roesing, N., Meilinger, D., Rothbauer, U., Cardoso, M.C. 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., Peluso, D., Gherardini, P.F., Rinaldis, E.D., Colombo, T., 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., Wurst, W. and Kühn, 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., Estibeiro, P., Wear, M.A., Max, K.E., Heinemann, U., Cubeddu, L., Gallagher, M.P., 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., Kuemmel, D., Soumailakakis, D., 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., Weber, P., Mayer, C., Graf, C., Refojo, D., Kühn, R., Grummt, I. and Lutz, B.
Nucleic Acids Research 35 (2): e10. January 2007

UniHI: an entry gate to the human protein interactome.
Chaurasia, G., Iqbal, Y., Haenig, C., Herzel, H., 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., 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., Roeseler, W., 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., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Buillard, V., Cerutti, L., Copley, R., Courcelle, E., Das, U., Daugherty, L., Dibley, M., Finn, R., Fleischmann, W., Gough, J., Haft, D., Hulo, N., Hunter, S., Kahn, D., Kanapin, A., Kejariwal, A., Labarga, A., Langendijk-Genevaux, P.S., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J.D., Sigrist, C.J., Thomas, P.D., Valentin, F., Wilson, D., 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., Jensen, L.J., Kuhn, M., Chaffron, S., Doerks, T., Krueger, B., 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., Rothbauer, U., 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., 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., 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., Copley, R.R., Pils, B., Pinkert, S., 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., Max, K.E.A., Weininger, U., Loew, C., 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., Bloch, I., 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., Domaing, P., 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., Küter-Luks, B., Kern, H., Streu, S., Plum, L., Mauer, J., Kühn, R., 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., Campillos, M., Harrington, E.D., Torrents, D. and Bork, P.
Nucleic Acids Research 33 (3): 946-954. 16 February 2005

InterPro, progress and status in 2005.
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Pagni, M., Ponting, C.P., Quevillon, E., Selengut, J., Sigrist, C.J., Silventoinen, V., Studholme, D.J., 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., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., 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., 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., Meyer, I.M., Forsberg, R., 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., Lagarde, J., 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., Pratto, F., Misselwitz, R., Speck, C., Weihofen, W., Welfle, K., Saenger, W., 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., Copley, R.R., Schmidt, S., Ciccarelli, F.D., Doerks, T., Schultz, J., 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., Herrmann, A., 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., Izsvak, Z., 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., Perez, A.J., 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., Linding, R., Gemund, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D.M.A., Ausiello, G., Brannetti, B., Costantini, A., Ferre, F., Maselli, V., Via, A., Cesareni, G., Diella, F., Superti-Furga, G., Wyrwicz, L., Ramu, C., McGuigan, C., Gudavalli, R., Letunic, I., Bork, P., Rychlewski, L., Kuester, B., Helmer-Citterich, M., Hunter, W.N., 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

MALDI mass spectrometry analysis of single nucleotide polymorphisms by photocleavage and charge-tagging.
Sauer, S., Lehrach, H. and Reinhardt, R.
Nucleic Acids Research 31 (11): e63. 1 June 2003

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

Rapid generation of inducible mouse mutants.
Seibler, J., Zevnik, B., Küter-Luks, B., Andreas, S., Kern, H., Hennek, T., Rode, A., Heimann, C., Faust, N., Kauselmann, G., Schoor, M., Jaenisch, R., Rajewsky, K., Kühn, 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., Apweiler, R., Attwood, T.K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R.R., Courcelle, E., Das, U., Durbin, R., Falquet, L., Fleischmann, W., Griffiths-Jones, S., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Lonsdale, D., Silventoinen, V., Orchard, S.E., Pagni, M., Peyruc, D., Ponting, C.P., Selengut, J.D., Servant, F., Sigrist, C.J.A., 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., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P. and Snel, B.
Nucleic Acids Research 31 (1): 258-261. 1 January 2003

CORG: a database for COmparative Regulatory Genomics.
Dieterich, C., Wang, H., Rateitschak, K., 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., Wende, W., Pingoud, A. and Heinemann, U.
Nucleic Acids Research 30 (18): 3962-3971. 15 September 2002

Human non-synonymous SNPs: server and survey.
Ramensky, V., 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., Reich, S., Muecke, M., Reuter, M., Messer, W., 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., Schwenk, F., Kueter-Luks, B., Faust, N. and Kühn, 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., Behlke, J., Brantl, S. and Lorenz, M.
Nucleic Acids Research 30 (9): 2052-2060. 1 May 2002

Two self-splicing group I introns in the ribonucleotide reductase large subunit gene of Staphylococcus aureus phage Twort.
Landthaler, M., Begley, U., Lau, N.C. and Shub, D.A.
Nucleic Acids Research 30 (9): 1935-1943. 1 March 2002

Facile method for automated genotyping of single nucleotide polymorphisms by mass spectrometry.
Sauer, S., Gelfand, D.H., Boussicault, F., Bauer, K., Reichert, F. and Gut, I.G.
Nucleic Acids Research 30 (5): e22. 1 March 2002

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
Fredman, D., Siegfried, M., Yuan, Y.P., Bork, P., 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., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P. and Bork, P.
Nucleic Acids Research 30 (1): 242-244. 1 January 2002

2000

Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay.
Sauer, S., Lechner, D., Berlin, K., Plançon, C., Heuermann, A., Lehrach, H. and Gut, I.G.
Nucleic Acids Research 28 (23): e100. 1 December 2000

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
Snel, B., Lehmann, G., 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., Huynen, M.A., Regula, J., Ueberle, B., Zimmermann, C.U., Andrade, M.A., Doerks, T., Sanches-Pulido, L., Snel, B., Suyama, M., Yuan, Y.P., 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., Finnegan, D. and Bucheton, A.
Nucleic Acids Research 28 (13): 2467-2472. 1 July 2000

A novel procedure for efficient genotyping of single nucleotide polymorphisms.
Sauer, S., Lechner, D., Berlin, K., Lehrach, H., Escary, J.L., Fox, N. and Gut, I.G.
Nucleic Acids Research 28 (5): e13. 1 March 2000

HGBASE: a database of SNPs and other variations in and around human genes.
Brookes, A.J., Lehvaslaiho, H., Siegfried, M., Boehm, J.G., Yuan, Y.P., Sarkar, C.M., 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., Copley, R.R., Doerks, T., 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., Schultz, J., 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., Fekete, M., Flamm, C., Huynen, M.A., Rauscher, S., 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., 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., 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., Kühn, R., Angrand, P.O., 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., Rabes, J.P., Thiart, R., Kotze, M.J., Baron, H., Cenarro, A., Descamps, O., Ebhardt, M., Hondelijn, J.C., Kostner, G.M., Miyake, Y., Pocovi, M., Schmidt, H., Schuster, H., Stuhrmann, M., Yamamura, T., Junien, C., 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., Hatada, E.N., 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., 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., 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., Sandig, V., Vooijs, M., van der Valk, M., Giovannini, M., 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., Behlke, J., 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., Warnecke, G., 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., Freundlieb, S., 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., 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., 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., Larin, Z., Montoliu, L., Thies, E., Kelsey, G., 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., Mueller, H., Reich, J., Riedel, H., Ahrenkiel, V., 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., 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., Hoelzer, W., Heinemann, U., 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., Kruft, V., Bobkova, E.V., 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., Sellmann, E., Kaluza, K., Frey, B., Auer, J., 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., Knoblich, I.M., Kaluza, K., Frey, B., 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., Ziegelin, G., Pansegrau, W., 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., Royer-Pokora, B., Delius, H., Kisseljov, F., Jenkins, N.A., Gilbert, D.J., 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., Hunter, J.B., Hennig, M. and Mueller, R.
Nucleic Acids Research 19 (4): 739-746. 25 February 1991