Works matching AU Zimmer, Ralf

Results: 89

RelExplain--integrating data and networks to explain biological processes.

Published in:

Bioinformatics, 2017, v. 33, n. 12, p. 1837, doi. 10.1093/bioinformatics/btx060

By:

Berchtold, Evi;
Csaba, Gergely;
Zimmer, Ralf

Publication type:

Article

Addressing false discoveries in network inference.

Published in:

Bioinformatics, 2015, v. 31, n. 17, p. 2836, doi. 10.1093/bioinformatics/btv215

By:

Petri, Tobias;
Altmann, Stefan;
Geistlinger, Ludwig;
Zimmer, Ralf;
Kuffner, Robert

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

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

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

Antiviral activity of the mineralocorticoid receptor NR3C2 against Herpes simplex virus Type 1 (HSV-1) infection.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-34241-w

By:

Haas, Jürgen G.;
Weber, Julia;
Gonzalez, Orland;
Zimmer, Ralf;
Griffiths, Samantha J.

Publication type:

Article

Experiment and mathematical modeling of gene expression dynamics in a cell-free system.

Published in:

Integrative Biology, 2012, v. 4, n. 5, p. 494, doi. 10.1039/c2ib00102k

By:

Stögbauer, Tobias;
Windhager, Lukas;
Zimmer, Ralf;
Rädler, Joachim O.

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

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

Inactivation of Intergenic Enhancers by EBNA3A Initiates and Maintains Polycomb Signatures across a Chromatin Domain Encoding CXCL10 and CXCL9.

Published in:

PLoS Pathogens, 2013, v. 9, n. 9, p. 1, doi. 10.1371/journal.ppat.1003638

By:

Harth-Hertle, Marie L.;
Scholz, Barbara A.;
Erhard, Florian;
Glaser, Laura V.;
Dölken, Lars;
Zimmer, Ralf;
Kempkes, Bettina

Publication type:

Article

A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication.

Published in:

PLoS Pathogens, 2013, v. 9, n. 8, p. 1, doi. 10.1371/journal.ppat.1003514

By:

Griffiths, Samantha J.;
Koegl, Manfred;
Boutell, Chris;
Zenner, Helen L.;
Crump, Colin M.;
Pica, Francesca;
Gonzalez, Orland;
Friedel, Caroline C.;
Barry, Gerald;
Martin, Kim;
Craigon, Marie H.;
Chen, Rui;
Kaza, Lakshmi N.;
Fossum, Even;
Fazakerley, John K.;
Efstathiou, Stacey;
Volpi, Antonio;
Zimmer, Ralf;
Ghazal, Peter;
Haas, Jürgen

Publication type:

Article

Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection.

Published in:

PLoS Pathogens, 2012, v. 8, n. 9, p. 1, doi. 10.1371/journal.ppat.1002908

By:

Marcinowski, Lisa;
Lidschreiber, Michael;
Windhager, Lukas;
Rieder, Martina;
Bosse, Jens B.;
Rädle, Bernd;
Bonfert, Thomas;
Györy, Ildiko;
De Graaf, Miranda;
Da Costa, Olivia Prazeres;
Rosenstiel, Philip;
Friedel, Caroline C.;
Zimmer, Ralf;
Ruzsics, Zsolt;
Dölken, Lars

Publication type:

Article

Degradation of Cellular miR-27 by a Novel, Highly Abundant Viral Transcript Is Important for Efficient Virus Replication In Vivo.

Published in:

PLoS Pathogens, 2012, v. 8, n. 2, p. 1, doi. 10.1371/journal.ppat.1002510

By:

Marcinowski, Lisa;
Tanguy, Mélanie;
Krmpotic, Astrid;
Rädle, Bernd;
Lisnić, Vanda J.;
Tuddenham, Lee;
Chane-Woon-Ming, Béatrice;
Ruzsics, Zsolt;
Erhard, Florian;
Benkartek, Corinna;
Babic, Marina;
Zimmer, Ralf;
Trgovcich, Joanne;
Koszinowski, Ulrich H.;
Jonjic, Stipan;
Dölken, Lars;
Pfeffer, Sébastien

Publication type:

Article

The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors.

Published in:

PLoS Pathogens, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.ppat.1002331

By:

Pfefferle, Susanne;
Schöpf, Julia;
Kögl, Manfred;
Friedel, Caroline C.;
Müller, Marcel A.;
Carbajo-Lozoya, Javier;
Stellberger, Thorsten;
von Dall'Armi, Ekatarina;
Herzog, Petra;
Kallies, Stefan;
Niemeyer, Daniela;
Ditt, Vanessa;
Kuri, Thomas;
Züst, Roland;
Pumpor, Ksenia;
Hilgenfeld, Rolf;
Schwarz, Frank;
Zimmer, Ralf;
Steffen, Imke;
Weber, Friedemann

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

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

A Loss of Function Analysis of Host Factors Influencing <i>Vaccinia virus</i> Replication by RNA Interference.

Published in:

PLoS ONE, 2014, v. 9, n. 6, p. 1, doi. 10.1371/journal.pone.0098431

By:

Beard, Philippa M.;
Griffiths, Samantha J.;
Gonzalez, Orland;
Haga, Ismar R.;
Pechenick Jowers, Tali;
Reynolds, Danielle K.;
Wildenhain, Jan;
Tekotte, Hille;
Auer, Manfred;
Tyers, Mike;
Ghazal, Peter;
Zimmer, Ralf;
Haas, Jürgen

Publication type:

Article

Mining RNA–Seq Data for Infections and Contaminations.

Published in:

PLoS ONE, 2013, v. 8, n. 9, p. 1, doi. 10.1371/journal.pone.0073071

By:

Bonfert, Thomas;
Csaba, Gergely;
Zimmer, Ralf;
Friedel, Caroline C.

Publication type:

Article

Complementing the Eukaryotic Protein Interactome.

Published in:

PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0066635

By:

Pesch, Robert;
Zimmer, Ralf

Publication type:

Article

MIRTFnet: Analysis of miRNA Regulated Transcription Factors.

Published in:

PLoS ONE, 2011, v. 6, n. 8, p. 1, doi. 10.1371/journal.pone.0022519

By:

Naeem, Haroon;
Küffner, Robert;
Zimmer, Ralf

Publication type:

Article

Petri Nets with Fuzzy Logic (PNFL): Reverse Engineering and Parametrization.

Published in:

PLoS ONE, 2010, v. 5, n. 9, p. 1, doi. 10.1371/journal.pone.0012807

By:

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

Publication type:

Article

Transcript-Specific Expression Profiles Derived from Sequence-Based Analysis of Standard Microarrays.

Published in:

PLoS ONE, 2009, v. 4, n. 3, p. 1, doi. 10.1371/journal.pone.0004702

By:

Moll, Anton G.;
Lindenmeyer, Maja T.;
Kretzler, Matthias;
Nelson, Peter J.;
Zimmer, Ralf;
Cohen, Clemens D.

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

ContextMap 2: fast and accurate context-based RNA-seq mapping.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0557-5

By:

Bonfert, Thomas;
Kirner, Evelyn;
Csaba, Gergely;
Zimmer, Ralf;
Friedel, Caroline C.

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