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Ralf Herwig

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Oligonucleotide Array Sequence Analysis

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Christina Grimm; Phillip Grote; Bernhard G Herrmann; Ralf Herwig; Hans Lehrach; Matthias Lienhard; Julia W Böhm; Lukas Chavez; Jörn Dietrich; Alexandra L Farrall; Michal R Schweiger; Sascha Tierling; Bernd Timmermann; Mireia Vilardell; Jörn Walter; Markus Morkel
DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer.
Bernhard Suter; Blanca M Vázquez-Álvarez; Reha Yildirimman; Martina Zenkner; Miguel Andrade; Jean-Fred Fontaine; Raphaele Foulle; Ralf Herwig; Pablo Porras; Axel Rasche; Tamás Raskó; Kirstin Rau; Jenny Russ; Kathrin Saar; Martin H Schaefer; Erich E Wanker
Development and application of a DNA microarray-based yeast two-hybrid system.
Marie-Laure Fogeron; Johan Gobom; Ralf Herwig; Karl Kashofer; Anne Kühnel; Felix Dreher; Beatrix Fauler; Verena Lehmann; Hans Lehrach; Rudi Lurz; Hannah Müller; Eckhard Nordhoff; Sophia Schade; Anne-Kathrin Scholz; Kurt Zatloukal; Alexandra Zerck; Bodo M H Lange
LGALS3BP regulates centriole biogenesis and centrosome hypertrophy in cancer cells.

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All Publications

2013: Christina Grimm; Phillip Grote; Bernhard G Herrmann; Ralf Herwig; Hans Lehrach; Matthias Lienhard; Julia W Böhm; Lukas Chavez; Jörn Dietrich; Alexandra L Farrall; Michal R Schweiger; Sascha Tierling; Bernd Timmermann; Mireia Vilardell; Jörn Walter; Markus Morkel
DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer.
PLoS genetics 2013;9(2):e1003250.
2013: Bernhard Suter; Blanca M Vázquez-Álvarez; Reha Yildirimman; Martina Zenkner; Miguel Andrade; Jean-Fred Fontaine; Raphaele Foulle; Ralf Herwig; Pablo Porras; Axel Rasche; Tamás Raskó; Kirstin Rau; Jenny Russ; Kathrin Saar; Martin H Schaefer; Erich E Wanker
Development and application of a DNA microarray-based yeast two-hybrid system.
Nucleic acids research 2013;41(3):1496-507.
2013: Marie-Laure Fogeron; Johan Gobom; Ralf Herwig; Karl Kashofer; Anne Kühnel; Felix Dreher; Beatrix Fauler; Verena Lehmann; Hans Lehrach; Rudi Lurz; Hannah Müller; Eckhard Nordhoff; Sophia Schade; Anne-Kathrin Scholz; Kurt Zatloukal; Alexandra Zerck; Bodo M H Lange
LGALS3BP regulates centriole biogenesis and centrosome hypertrophy in cancer cells.
Nature communications 2013;4():1531.
2013: Atanas Kamburov; Hans Lehrach; Ulrich Stelzl; Ralf Herwig
The ConsensusPathDB interaction database: 2013 update.
Nucleic acids research 2013;41(Database issue):D793-800.
2012: Christoph Wierling; Jian Li; Elisabeth Maschke-Dutz; Svetlana Peycheva; Andriani Daskalaki; Hendrik Hache; Ralf Herwig; Alexander Kühn; Hans Lehrach
Prediction in the face of uncertainty: a Monte Carlo-based approach for systems biology of cancer treatment.
Mutation research 2012;746(2):163-70.
2012: Atanas Kamburov; Ulrich Stelzl; Ralf Herwig
IntScore: a web tool for confidence scoring of biological interactions.
Nucleic acids research 2012;40(Web Server issue):W140-6.
2012: Atanas Kamburov; Arndt Grossmann; Ralf Herwig; Ulrich Stelzl
Cluster-based assessment of protein-protein interaction confidence.
BMC bioinformatics 2012;13():262.
2012: Felix Dreher; Christopher Hardt; Atanas Kamburov; Thomas Kreitler; Bodo M H Lange; Hans Lehrach; Karl Schellander; Reha Yildirimman; Ralf Herwig
DIPSBC--data integration platform for systems biology collaborations.
BMC bioinformatics 2012;13():85.
2012: Felix Dreher; Atanas Kamburov; Ralf Herwig
Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactome.
Evolutionary bioinformatics online 2012;8():119-26.
2011: Reha Yildirimman; Petter Björquist; Gabriella Brolén; José Castell; Gustav Eriksson; Hans Gmuender; Magnus Ingelman-Sundberg; Atanas Kamburov; Jos Kleinjans; Agustin Lahoz; Jane Synnergren; Joost van Delft; Mireia Vilardell; Ralf Herwig
Human embryonic stem cell derived hepatocyte-like cells as a tool for in vitro hazard assessment of chemical carcinogenicity.
Toxicological sciences : an official journal of the Society of Toxicology 2011;124(2):278-90.
2011: Atanas Kamburov; Rachel Cavill; Timothy M D Ebbels; Ralf Herwig; Hector C Keun
Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA.
Bioinformatics (Oxford, England) 2011;27(20):2917-8.
2011: Hannah Müller; Aspasia Ploubidou; David Schmidt; Felix Dreher; Ralf Herwig; Bodo M H Lange
Gene ontology analysis of the centrosome proteomes of Drosophila and human.
Communicative & integrative biology 2011;4(3):308-11.
2011: Thomas Meinel; Michal R Schweiger; Ramu Chenna; Sylvia Krobitsch; Andreas H Ludewig; Ralf Herwig
Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information.
BMC genomics 2011;12():483.
2011: Martin Kerick; Helmut Klocker; Sylvia Krobitsch; Hans Lehrach; Georg Schaefer; Georg Bartsch; Ralf Herwig; Melanie Isau; Holger Sültmann; Bernd Timmermann; Irmgard Verdorfer; Michal R Schweiger
Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity.
BMC medical genomics 2011;4():68.
2011: Mireia Vilardell; Hans Lehrach; Elisabeth Maschke-Dutz; Luis A Pérez Jurado; Axel Rasche; Anja Thormann; Ralf Herwig
Meta-analysis of heterogeneous Down Syndrome data reveals consistent genome-wide dosage effects related to neurological processes.
BMC genomics 2011;12():229.
2011: Atanas Kamburov; Konstantin Pentchev; Hanna Galicka; Christoph Wierling; Hans Lehrach; Ralf Herwig
ConsensusPathDB: toward a more complete picture of cell biology.
Nucleic acids research 2011;39(Database issue):D712-7.
2010: Konstantin Pentchev; Keiichiro Ono; Ralf Herwig; Trey Ideker; Atanas Kamburov
Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape.
Bioinformatics (Oxford, England) 2010;26(21):2796-7.
2010: Hannah Müller; David Schmidt; Sandra Steinbrink; Ekaterina Mirgorodskaya; Verena Lehmann; Karin Habermann; Felix Dreher; Niklas Gustavsson; Thomas Kessler; Hans Lehrach; Ralf Herwig; Johan Gobom; Aspasia Ploubidou; Michael Boutros; Bodo M H Lange
Proteomic and functional analysis of the mitotic Drosophila centrosome.
The EMBO journal 2010;29(19):3344-57.
2010: Lukas Chavez; Justyna Jozefczuk; Christina Grimm; Jörn Dietrich; Bernd Timmermann; Hans Lehrach; Ralf Herwig; James Adjaye
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage.
Genome research 2010;20(10):1441-50.
2010: Justyna Jozefczuk; Harald Stachelscheid; Lukas Chavez; Ralf Herwig; Hans Lehrach; Katrin Zeilinger; Jörg C Gerlach; James Adjaye
Molecular characterization of cultured adult human liver progenitor cells.
Tissue engineering. Part C, Methods 2010;16(5):821-34.
2010: Axel Rasche; Ralf Herwig
ARH: predicting splice variants from genome-wide data with modified entropy.
Bioinformatics (Oxford, England) 2010;26(1):84-90.
2009: Seyed S Dianat; Markus Margreiter; Elisabeth Eckersberger; Julia Finkelstein; Franklin Kuehas; Ralf Herwig; Mohsen Ayati; Herbert Lepor; Bob Djavan
Gene polymorphisms and prostate cancer: the evidence.
BJU international 2009;104(11):1560-72.
2009: Hendrik Hache; Christoph Wierling; Hans Lehrach; Ralf Herwig
GeNGe: systematic generation of gene regulatory networks.
Bioinformatics (Oxford, England) 2009;25(9):1205-7.
2009: Lukas Chavez; Abha S Bais; Martin Vingron; Hans Lehrach; Christian Regenbrecht; Ralf Herwig
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach.
BMC genomics 2009;10():314.
2009: Hendrik Hache; Hans Lehrach; Ralf Herwig
Reverse engineering of gene regulatory networks: a comparative study.
EURASIP journal on bioinformatics & systems biology 2009;():617281.
2008: Axel Rasche; Hadi Al-Hasani; Ralf Herwig
Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus.
BMC genomics 2008;9():310.
2007: Christian Regenbrecht; Ralf Herwig; Thore C Brink; Doris Herrmann; Boris Greber; Smita Sudheer; Detlef Groth; Joseph W Carnwath; Hans Lehrach; Heiner Niemann
Conserved molecular portraits of bovine and human blastocysts as a consequence of the transition from maternal to embryonic control of gene expression.
Physiological genomics 2007;31(2):315-27.
2007: Christoph Wierling; Ralf Herwig; Hans Lehrach
Resources, standards and tools for systems biology.
Briefings in functional genomics & proteomics 2007;6(3):240-51.
2007: Jian-Ping Liu; Mario Drungowski; Lajos Nyársik; Regine Schwartz; Hans Lehrach; Ralf Herwig; Michal Janitz
Oligonucleotide fingerprinting of arrayed genomic DNA sequences using LNA-modified hybridization probes.
Combinatorial chemistry & high throughput screening 2007;10(4):269-76.
2007: James T Bennett; Katherine Joubin; Simon Cheng; Pia Aanstad; Ralf Herwig; Matthew Clark; Hans Lehrach; Alexander F Schier
Nodal signaling activates differentiation genes during zebrafish gastrulation.
Developmental biology 2007;304(2):525-40.
2007: Yasmin Babaie; Ralf Herwig; Boris Greber; Thore C Brink; Wasco Wruck; Detlef Groth; Hans Lehrach; Tom Burdon; Christian Regenbrecht
Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells.
Stem cells (Dayton, Ohio) 2007;25(2):500-10.
2007: Marc Sultan; Ilaria Piccini; Daniela Balzereit; Ralf Herwig; Nidhi G Saran; Hans Lehrach; Roger H Reeves; Marie-Laure Yaspo
Gene expression variation in Down's syndrome mice allows prioritization of candidate genes.
Genome biology 2007;8(5):R91.
2007: Annemarie Poustka; Alexander Kühn; Detlef Groth; Vesna Weise; Shunsuke Yaguchi; Robert D Burke; Ralf Herwig; Hans Lehrach; Georgia Panopoulou
A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks.
Genome biology 2007;8(5):R85.
2006: Evgenia Makrantonaki; Christian Regenbrecht; Ralf Herwig; Thore C Brink; Detlef Groth; Claus Hultschig; Hans Lehrach; Christos Zouboulis
Age-specific hormonal decline is accompanied by transcriptional changes in human sebocytes in vitro.
Aging cell 2006;5(4):331-44.
2006: Ralf Herwig; Hans Lehrach
Expression profiling of drug response--from genes to pathways.
Dialogues in clinical neuroscience 2006;8(3):283-93.
2006: Oliver C Jann; Jan Aerts; Michelle Jones; Nicola Hastings; Andy Law; Stephanie McKay; Elisa Marques; APARNA PRASAD; Jody Yu; Stephen S Moore; Sandrine Floriot; Marie-Françoise Mahé; André Eggen; Licia Silveri; Riccardo Negrini; Elisabetta Milanesi; Paolo Ajmone-Marsan; Alessio Valentini; Cinzia Marchitelli; Maria C Savarese; Michal Janitz; Ralf Herwig; Steffen Hennig; Chiara Gorni; Erin E Connor; Tad S Sonstegard; Timothy Smith; Cord Drögemüller; John L Williams
A second generation radiation hybrid map to aid the assembly of the bovine genome sequence.
BMC genomics 2006;7():283.
2006: Evgenia Makrantonaki; Christian Regenbrecht; Ralf Herwig; Thore C Brink; Detlef Groth; Claus Hultschig; Hans Lehrach; Christos Zouboulis
Aging of human sebocytes in vitro induced by exposure to a defined hormone environment.
Dermatology (Basel, Switzerland) 2006;213(3):262-3.
2005: Christian Regenbrecht; John Huntriss; Ralf Herwig; Alia Benkahla; Thore C Brink; Christoph Wierling; Claus Hultschig; Detlef Groth; Marie-Laure Yaspo; Helen M Picton; Roger G Gosden; Hans Lehrach
Primary differentiation in the human blastocyst: comparative molecular portraits of inner cell mass and trophectoderm cells.
Stem cells (Dayton, Ohio) 2005;23(10):1514-25.
2005: Eleni Papakonstantinou; Alexios J Aletras; Evelyn Glass; Panagiotis Tsogas; Alexander Dionyssopoulos; Christian Regenbrecht; Sabine Fimmel; Panagiotis Gouvousis; Ralf Herwig; Hans Lehrach; Christos Zouboulis; George Karakiulakis
Matrix metalloproteinases of epithelial origin in facial sebum of patients with acne and their regulation by isotretinoin.
The Journal of investigative dermatology 2005;125(4):673-84.
2005: Witold Eryk Wolski; Maciej Lalowski; Peter Martus; Ralf Herwig; Patrick Giavalisco; Johan Gobom; Albert Sickmann; Hans Lehrach; Knut Reinert
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process.
BMC bioinformatics 2005;6():285.
2004: J Illiger; Ralf Herwig; Matthias Steinfath; T Przewieslik; Thorsten Elge; Ch Bull; Uwe Radelof; Hans Lehrach; Michal Janitz
Establishment of T cell-specific and natural killer cell-specific unigene sets: towards high-throughput genomics of leukaemia.
European journal of immunogenetics : official journal of the British Society for Histocompatibility and Immunogenetics 2004;31(6):253-7.
2004: Christian Regenbrecht; Ralf Herwig; Doris Herrmann; Wasco Wruck; Alia Benkahla; Thore C Brink; Monika Nowak; Joseph W Carnwath; Claus Hultschig; Heiner Niemann; Hans Lehrach
Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays.
BMC genomics 2004;5():83.
2004: Pascal Kahlem; Marc Sultan; Ralf Herwig; Matthias Steinfath; Daniela Balzereit; Barbara Eppens; Nidhi G Saran; Mathew Pletcher; Sarah T South; Gail Stetten; Hans Lehrach; Roger H Reeves; Marie-Laure Yaspo
Transcript level alterations reflect gene dosage effects across multiple tissues in a mouse model of down syndrome.
Genome research 2004;14(7):1258-67.
2004: Thomas Dickmeis; Charles Plessy; Sepand Rastegar; Pia Aanstad; Ralf Herwig; Frédéric Chalmel; Nadine Fischer; Uwe Strähle
Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo.
Genome research 2004;14(2):228-38.
2004: Oliver Bauer; Anna Guerasimova; Sascha Sauer; Sabine Thamm; Matthias Steinfath; Ralf Herwig; Michal Janitz; Hans Lehrach; Uwe Radelof
Multiplexed hybridizations of positively charge-tagged peptide nucleic acids detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
Rapid communications in mass spectrometry : RCM 2004;18(16):1821-9.
2003: Annemarie Poustka; Detlef Groth; Steffen Hennig; Sabine Thamm; Andrew Cameron; Alfred Beck; Richard Reinhardt; Ralf Herwig; Georgia Panopoulou; Hans Lehrach
Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters.
Genome research 2003;13(12):2736-46.
2003: Christoph Dieterich; Ralf Herwig; Martin Vingron
Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites.
Bioinformatics (Oxford, England) 2003;19 Suppl 2():ii50-6.
2003: Georgia Panopoulou; Steffen Hennig; Detlef Groth; Antje Krause; Annemarie Poustka; Ralf Herwig; Martin Vingron; Hans Lehrach
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes.
Genome research 2003;13(6A):1056-66.
2002: Yorick Gitton; Nadia Dahmane; Sonya Baik; Ariel Ruiz i Altaba; Lorenz Neidhardt; Manuela Scholze; Bernhard G Herrmann; Pascal Kahlem; Alia Benkahla; Sabine Schrinner; Reha Yildirimman; Ralf Herwig; Hans Lehrach; Marie-Laure Yaspo
A gene expression map of human chromosome 21 orthologues in the mouse.
Nature 2002;420(6915):586-90.
2002: Ralf Herwig; Britta Schulz; Bernd Weisshaar; Steffen Hennig; Matthias Steinfath; Mario Drungowski; Dietmar Stahl; Wasco Wruck; Andreas Menze; John O'Brien; Hans Lehrach; Uwe Radelof
Construction of a 'unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genes.
The Plant journal : for cell and molecular biology 2002;32(5):845-57.
2002: Christoph Wierling; Matthias Steinfath; Thorsten Elge; Steffen Schulze-Kremer; Pia Aanstad; Matthew Clark; Hans Lehrach; Ralf Herwig
Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis.
BMC bioinformatics 2002;3():29.
2002: Tania Fuchs; Barbora Malecova; Chaim Linhart; Roded Sharan; Miriam Khen; Ralf Herwig; Dmitry Shmulevich; Ran Elkon; Matthias Steinfath; John K O'Brien; Uwe Radelof; Hans Lehrach; Doron Lancet; Ron Shamir
DEFOG: a practical scheme for deciphering families of genes.
Genomics 2002;80(3):295-302.
2001: Thomas Dickmeis; Pia Aanstad; Matthew Clark; Nadine Fischer; Ralf Herwig; Philippe Mourrain; Patrick Blader; Frédéric M Rosa; Hans Lehrach; Uwe Strähle
Identification of nodal signaling targets by array analysis of induced complex probes.
Developmental dynamics : an official publication of the American Association of Anatomists 2001;222(4):571-80.
2001: Ralf Herwig; Pia Aanstad; Matthew Clark; Hans Lehrach
Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments.
Nucleic acids research 2001;29(23):E117.
2001: Anna Guerasimova; Lajos Nyarsik; I Girnus; Matthias Steinfath; Wasco Wruck; H Griffiths; Ralf Herwig; Christoph Wierling; John O'Brien; Holger Eickhoff; Hans Lehrach; Uwe Radelof
New tools for oligonucleotide fingerprinting.
BioTechniques 2001;31(3):490-5.
2001: Matthew Clark; Steffen Hennig; Ralf Herwig; S W Clifton; M A Marra; Hans Lehrach; S L Johnson
An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library.
Genome research 2001;11(9):1594-602.
2000: Ralf Herwig; A O Schmitt; Matthias Steinfath; John O'Brien; H Seidel; S Meier-Ewert; Hans Lehrach; Uwe Radelof
Information theoretical probe selection for hybridisation experiments.
Bioinformatics (Oxford, England) 2000;16(10):890-8.
1999: Ralf Herwig; A J Poustka; C Müller; C Bull; Hans Lehrach; John O'Brien
Large-scale clustering of cDNA-fingerprinting data.
Genome research 1999;9(11):1093-105.
1999: Annemarie Poustka; Ralf Herwig; A Krause; Steffen Hennig; S Meier-Ewert; Hans Lehrach
Toward the gene catalogue of sea urchin development: the construction and analysis of an unfertilized egg cDNA library highly normalized by oligonucleotide fingerprinting.
Genomics 1999;59(2):122-33.
1998: S Meier-Ewert; J Lange; H Gerst; Ralf Herwig; A Schmitt; J Freund; Thorsten Elge; R Mott; B Herrmann; Hans Lehrach
Comparative gene expression profiling by oligonucleotide fingerprinting.
Nucleic acids research 1998;26(9):2216-23.