Works by Zimmer, Ralf

Results: 89

Pathway analysis in metabolic databases via differential metabolic display (DMD).

Published in:

Bioinformatics, 2000, v. 16, n. 9, p. 825, doi. 10.1093/bioinformatics/16.9.825

By:

Küffner, Robert;
Zimmer, Ralf;
Lengauer, Thomas

Publication type:

Article

New scoring schemes for protein fold recognition based on Voronoi contacts.

Published in:

Bioinformatics, 1998, v. 14, n. 3, p. 295, doi. 10.1093/bioinformatics/14.3.295

By:

Zimmer, Ralf;
Wöhler, Marko;
Thiele, Ralf

Publication type:

Article

ProML - The Protein Markup Language for Specification of Protein Sequences, Structures and Families.

Published in:

In Silico Biology, 2002, v. 2, n. 3, p. 313

By:

Hanisch, Daniel;
Zimmer, Ralf;
Lengauer, Thomas

Publication type:

Article

Improving Fold Recognition of Protein Threading by Experimental Distance Constraints.

Published in:

In Silico Biology, 2002, v. 2, n. 3, p. 325

By:

Albrecht, Mario;
Hanisch, Daniel;
Zimmer, Ralf;
Lengauer, Thomas

Publication type:

Article

A Hypergraph-Based Method for Unification of Existing Protein Structure- and Sequence-Families.

Published in:

In Silico Biology, 2002, v. 2, n. 3, p. 339

By:

Freudenberg, Jan;
Zimmer, Ralf;
Hanisch, Daniel;
Lengauer, Thomas

Publication type:

Article

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life.

Published in:

Nucleic Acids Research, 2009, v. 37, n. 17, p. e115, doi. 10.1093/nar/gkp542

By:

Friedel, Caroline C.;
Dölken, Lars;
Ruzsics, Zsolt;
Koszinowski, Ulrich H.;
Zimmer, Ralf

Publication type:

Article

Alternative splicing and protein structure evolution.

Published in:

Nucleic Acids Research, 2008, v. 36, n. 2, p. 550, doi. 10.1093/nar/gkm1054

By:

Birzele, Fabian;
Csaba, Gergely;
Zimmer, Ralf

Publication type:

Article

ProSAS: a database for analyzing alternative splicing in the context of protein structures.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D63

By:

Birzele, Fabian;
Küffner, Robert;
Meier, Franziska;
Oefinger, Florian;
Potthast, Christian;
Zimmer, Ralf

Publication type:

Article

AutoPSI: a database for automatic structural classification of protein sequences and structures.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D398

By:

Birzele, Fabian;
Gewehr, Jan E.;
Zimmer, Ralf

Publication type:

Article

PARma: identification of microRNA target sites in AGO-PAR-CLIP data

Published in:

Genome Biology, 2013, v. 14, n. 7, p. R79, doi. 10.1186/gb-2013-14-7-r79

By:

Erhard, Florian;
Dölken, Lars;
Jaskiewicz, Lukasz;
Zimmer, Ralf

Publication type:

Article

A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock.

Published in:

Biotechnology for Biofuels, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13068-019-1584-7

By:

Sedlar, Karel;
Kolek, Jan;
Gruber, Markus;
Jureckova, Katerina;
Branska, Barbora;
Csaba, Gergely;
Vasylkivska, Maryna;
Zimmer, Ralf;
Patakova, Petra;
Provaznik, Ivo

Publication type:

Article

Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis.

Published in:

BMC Structural Biology, 2009, v. 9, p. 1, doi. 10.1186/1472-6807-9-23

By:

Csaba, Gergely;
Birzele, Fabian;
Zimmer, Ralf

Publication type:

Article

miR-103 promotes endothelial maladaptation by targeting lncWDR59.

Published in:

Nature Communications, 2018, v. 9, p. 1, doi. 10.1038/s41467-018-05065-z

By:

Natarelli, Lucia;
Geißler, Claudia;
Csaba, Gergely;
Yuanyuan Wei;
Mengyu Zhu;
di Francesco, Andrea;
Hartmann, Petra;
Zimmer, Ralf;
Schober, Andreas

Publication type:

Article

Nachbarschaften in der Stadtentwicklung. Idealisierungen, Alltagsräume und professionelles Handlungswissen.

Published in:

Raumforschung und Raumordnung, 2023, v. 81, n. 2, p. 203, doi. 10.14512/rur.1713

By:

Zimmer-Hegmann, Ralf

Publication type:

Article

Wohnungsforschung. Ein Reader.

Published in:

Raumforschung und Raumordnung, 2021, v. 79, n. 6, p. 620, doi. 10.14512/rur.143

By:

Zimmer-Hegmann, Ralf

Publication type:

Article

Urbane Reallabore im Kontext von transdisziplinärer Stadtforschung und Planungswissenschaft.

Published in:

Raumforschung und Raumordnung, 2021, v. 79, n. 4, p. 287, doi. 10.14512/rur.139

By:

Räuchle, Charlotte;
Stelzer, Franziska;
Zimmer-Hegmann, Ralf

Publication type:

Article

Berndt, Patricia; Sinning, Heidi (2016): Images innenstadtnaher Wohnquartiere. Strategien zur Steuerung von Images als kooperative Aufgabe der Wohnungswirtschaft und Stadtentwicklung.

Published in:

2017

By:

Zimmer-Hegmann, Ralf

Publication type:

Book Review

Cross-species Conservation of context-specific networks.

Published in:

BMC Systems Biology, 2016, v. 10, p. 1, doi. 10.1186/s12918-016-0304-1

By:

Pesch, Robert;
Zimmer, Ralf

Publication type:

Article

A commonly used rumen-protected conjugated linoleic acid supplement marginally affects fatty acid distribution of body tissues and gene expression of mammary gland in heifers during early lactation.

Published in:

Lipids in Health & Disease, 2013, v. 12, n. 1, p. 1, doi. 10.1186/1476-511X-12-96

By:

Kramer, Ronny;
Wolf, Simone;
Petri, Tobias;
Soosten, Dirk von;
Dänicke, Sven;
Weber, Eva-Maria;
Zimmer, Ralf;
Rehage, Juergen;
Jahreis, Gerhard

Publication type:

Article

Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 6, p. 1, doi. 10.1371/journal.pcbi.1000799

By:

Gonzalez, Orland;
Oberwinkler, Tanja;
Mansueto, Locedie;
Pfeiffer, Friedhelm;
Mendoza, Eduardo;
Zimmer, Ralf;
Oesterhelt, Dieter

Publication type:

Article

Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 4, p. 1, doi. 10.1371/journal.pcbi.1000332

By:

Gonzalez, Orland;
Gronau, Susanne;
Pfeiffer, Friedhelm;
Mendoza, Eduardo;
Zimmer, Ralf;
Oesterhelt, Dieter

Publication type:

Article

Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data.

Published in:

PLoS ONE, 2016, v. 11, n. 10, p. 1, doi. 10.1371/journal.pone.0164513

By:

Berchtold, Evi;
Csaba, Gergely;
Zimmer, Ralf

Publication type:

Article

Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle.

Published in:

PLoS ONE, 2016, v. 11, n. 6, p. 1, doi. 10.1371/journal.pone.0157711

By:

Silva, Vinicius Henrique da;
Regitano, Luciana Correia de Almeida;
Geistlinger, Ludwig;
Pértille, Fábio;
Giachetto, Poliana Fernanda;
Brassaloti, Ricardo Augusto;
Morosini, Natália Silva;
Zimmer, Ralf;
Coutinho, Luiz Lehmann

Publication type:

Article

Detection of network motifs using three-way ANOVA.

Published in:

PLoS ONE, 2018, v. 13, n. 8, p. 1, doi. 10.1371/journal.pone.0201382

By:

Tavakkolkhah, Pegah;
Zimmer, Ralf;
Küffner, Robert

Publication type:

Article

Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival.

Published in:

Molecular Systems Biology, 2022, v. 18, n. 12, p. 1, doi. 10.15252/msb.202211160

By:

Schink, Severin;
Ammar, Constantin;
Chang, Yu‐Fang;
Zimmer, Ralf;
Basan, Markus

Publication type:

Article

Scenical Emotion centered Therapy of voice (SEST) – a new treatment approach for functional voice disorders.

Published in:

2012

By:

Zimmer, Ralf

Publication type:

Journal Article

Szenische Emotionszentrierte Stimmtherapie--SEST: Ein neuer Ansatz zur Behandlung funktioneller Stimmstörungen.

Published in:

Forum Logopadie, 2012, v. 26, n. 4, p. 6, doi. 10.2443/skv-s-2012-53020120401

By:

Zimmer, Ralf

Publication type:

Article

A Turing test for artificial expression data.

Published in:

Bioinformatics, 2013, v. 29, n. 20, p. 2603, doi. 10.1093/bioinformatics/btt438

By:

Maier, Robert;
Zimmer, Ralf;
Küffner, Robert

Publication type:

Article

RIP-chip enrichment analysis.

Published in:

Bioinformatics, 2013, v. 29, n. 1, p. 77, doi. 10.1093/bioinformatics/bts631

By:

Erhard, Florian;
Dölken, Lars;
Zimmer, Ralf

Publication type:

Article

Rigorous assessment of gene set enrichment tests.

Published in:

Bioinformatics, 2012, v. 28, n. 11, p. 1480, doi. 10.1093/bioinformatics/bts164

By:

Naeem, Haroon;
Zimmer, Ralf;
Tavakkolkhah, Pegah;
Küffner, Robert

Publication type:

Article

Inferring gene regulatory networks by ANOVA.

Published in:

Bioinformatics, 2012, v. 28, n. 10, p. 1376, doi. 10.1093/bioinformatics/bts143

By:

Küffner, Robert;
Petri, Tobias;
Tavakkolkhah, Pegah;
Windhager, Lukas;
Zimmer, Ralf

Publication type:

Article

Contextual analysis of RNAi-based functional screens using interaction networks.

Published in:

Bioinformatics, 2011, v. 27, n. 19, p. 2707, doi. 10.1093/bioinformatics/btr469

By:

Gonzalez, Orland;
Zimmer, Ralf

Publication type:

Article

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems.

Published in:

Bioinformatics, 2011, v. 27, n. 13, p. i366, doi. 10.1093/bioinformatics/btr228

By:

Geistlinger, Ludwig;
Csaba, Gergely;
Küffner, Robert;
Mulder, Nicola;
Zimmer, Ralf

Publication type:

Article

Vorescore—fold recognition improved by rescoring of protein structure models.

Published in:

Bioinformatics, 2010, v. 26, n. 18, p. i474, doi. 10.1093/bioinformatics/btq369

By:

Csaba, Gergely;
Zimmer, Ralf

Publication type:

Article

Classification of ncRNAs using position and size information in deep sequencing data.

Published in:

Bioinformatics, 2010, v. 26, n. 18, p. i426, doi. 10.1093/bioinformatics/btq363

By:

Erhard, Florian;
Zimmer, Ralf

Publication type:

Article

HALO—a Java framework for precise transcript half-life determination.

Published in:

Bioinformatics, 2010, v. 26, n. 9, p. 1264, doi. 10.1093/bioinformatics/btq117

By:

Friedel, Caroline C.;
Kaufmann, Stefanie;
Dölken, Lars;
Zimmer, Ralf;
Dopazo, Joaquin

Publication type:

Article

ProCope--protein complex prediction and evaluation.

Published in:

Bioinformatics, 2008, v. 24, n. 18, p. 2115, doi. 10.1093/bioinformatics/btn376

By:

Jan Krumsiek;
Caroline C. Friedel;
Ralf Zimmer

Publication type:

Article

Protein structure alignment considering phenotypic plasticity.

Published in:

Bioinformatics, 2008, v. 24, n. 16, p. i98, doi. 10.1093/bioinformatics/btn271

By:

Gergely Csaba;
Fabian Birzele;
Ralf Zimmer

Publication type:

Article

Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes.

Published in:

Bioinformatics, 2008, v. 24, n. 10, p. 1257, doi. 10.1093/bioinformatics/btn106

By:

Orland Gonzalez;
Ralf Zimmer

Publication type:

Article

AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings.

Published in:

Bioinformatics, 2007, v. 23, n. 10, p. 1203, doi. 10.1093/bioinformatics/btm089

By:

Jan E. Gewehr;
Volker Hintermair;
Ralf Zimmer

Publication type:

Article

Reliable gene signatures for microarray classification: assessment of stability and performance.

Published in:

Bioinformatics, 2006, v. 22, n. 19, p. 2356, doi. 10.1093/bioinformatics/btl400

By:

Davis, Chad A.;
Gerick, Fabian;
Hintermair, Volker;
Friedel, Caroline C.;
Fundel, Katrin;
Küffner, Robert;
Zimmer, Ralf

Publication type:

Article

Web servicing the biological office.

Published in:

Bioinformatics, 2005, v. 21, p. ii268, doi. 10.1093/bioinformatics/bti1144

By:

Szugat, Martin;
Güttler, Daniel;
Fundel, Katrin;
Sohler, Florian;
Zimmer, Ralf

Publication type:

Article

Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts.

Published in:

Bioinformatics, 2005, v. 21, p. ii259, doi. 10.1093/bioinformatics/bti1143

By:

Küffner, Robert;
Fundel, Katrin;
Zimmer, Ralf

Publication type:

Article

Identifying active transcription factors and kinases from expression data using pathway queries.

Published in:

Bioinformatics, 2005, v. 21, p. ii115, doi. 10.1093/bioinformatics/bti1120

By:

Sohler, Florian;
Zimmer, Ralf

Publication type:

Article

New methods for joint analysis of biological networks and expression data.

Published in:

Bioinformatics, 2004, v. 20, n. 10, p. 1517, doi. 10.1093/bioinformatics/bth112

By:

Florian Sohler;
Daniel Hanisch;
Ralf Zimmer

Publication type:

Article

ToPNet—an application for interactive analysis of expression data and biological networks.

Published in:

Bioinformatics, 2004, v. 20, n. 9, p. 1470, doi. 10.1093/bioinformatics/bth096

By:

Daniel Hanisch;
Florian Sohler;
Ralf Zimmer

Publication type:

Article

Co-clustering of biological networks and gene expression data.

Published in:

Bioinformatics, 2002, v. 18, p. S145, doi. 10.1093/bioinformatics/18.suppl_1.S145

By:

Hanisch, Daniel;
Zien, Alexander;
Zimmer, Ralf;
Lengauer, Thomas

Publication type:

Article

Confidence measures for protein fold recognition.

Published in:

Bioinformatics, 2002, v. 18, n. 6, p. 802, doi. 10.1093/bioinformatics/18.6.802

By:

Sommer, Ingolf;
Zien, Alexander;
von Öhsen, Niklas;
Zimmer, Ralf;
Lengauer, Thomas

Publication type:

Article

Centralization: a new method for the normalization of gene expression data.

Published in:

Bioinformatics, 2001, v. 17, p. 323, doi. 10.1093/bioinformatics/17.suppl_1.s323

By:

Zien, Alexander;
Aigner, Thomas;
Zimmer, Ralf;
Lengauer, Thomas

Publication type:

Article

Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis.

Published in:

BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-0884-1

By:

Geistlinger, Ludwig;
Csaba, Gergely;
Zimmer, Ralf

Publication type:

Article