Visit our Expo - Redox and Inflammation signaling 2012

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Molecular Networks in Mammals: Extraction from Literature and Pathway Analysis Ariadne Genomics, Inc. Using the proprietary high-content linguistics tool MedScan we compiled a comprehensive database of molecular networks by extracting the information from scientific literature. MedScan is capable of extracting functional associations between proteins, small molecules, and pathways, recognizes types of regulatory mechanisms involved, effects of regulation and experimental conditions. The resulting database stores 700,000 relationships between mammalian proteins and chemicals including facts about protein interactions, promoter binding, molecular biosynthesis and trafficking, and cell process regulation. Different approaches towards reconstructing individual pathways or cascades from this database and assigning functional categories to proteins will be described. Our visualization software is capable of systematically mining this database for small network motifs that are robust in regard to the effects induced at the gene expression levels. We have also developed a Bayesian framework for integration of microarray data and binary gene-togene regulatory relationships. The approach allows the reduction of expression pattern complexity and finds the minimal set of regulatory proteins that are responsible for differential expression of other genes. Finding mesoscopic communities in sparse networks I. Ispolatov, I. Mazo, and A. Yuryev q-bio.MN/0512038, submitted to Phys. Rev. E Identifying Local Gene Expression Patterns in Biomolecular Networks A. Y. Sivachenko, A. Yuryev, N. Daraselia, I. Mazo 2005 IEEE Computational Systems Bioinformatics Conference, Aug. 8-11, 2005 Cliques and duplication-divergence network growth Ispolatov, I ; Krapivsky, P L ; Mazo, I ; Yuryev, A New J.Phys. 7(2005) 145 Binding properties and evolution of homodimers in protein-protein interaction networks Ispolatov, Iaroslav; Yuryev, Anton; Mazo, Ilya; Maslov, Sergei Nucleic Acids Research 2005 33(11):3629-3635 Extracting Protein Function Information from MEDLINE Using a Full-Sentence Parser Nikolai Daraselia, Sergei Egorov, Andrey Yazhuk, Svetlana Novichkova, Anton Yuryev, Ilya Mazo published in Proceeding of the Second European Workshop on Data Mining and Text Mining for Bioinformatics, pp11-18, 2004 A Simple and Practical Dictionary-Based Approach for Identification of Proteins in MEDLINE Abstracts Sergei Egorov PhD, Anton Yuryev PhD, and Nikolai Daraselia PhD Journal of the American Medical Informatics Association 2004 Pathway studio - the analysis and navigation of molecular networks Alexander Nikitin, Sergei Egorov, Nikolai Daraselia and Ilya Mazo BIOINFORMATICS APPLICATIONS NOTE Vol. 19 no. 0 2003, pages 1-3 Extracting human protein interactions from MEDLINE using a full-sentence parser Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Svetalana Novichkova, Alexander Nikitin and Ilya Mazo BIOINFORMATICS Vol. 19 no. 0 2003, pages 1–8 - 110 -
Organizer: BIOBASE GmbH Date: January, 26 2006 Time: 3 pm – 4:30 pm Duration: ca 1 hour 30 minutes Attendees: 110 - 140 Topic: Cutting-edge Biology for Explaining Expression Data Chair: Alena Kemper, BIOBASE, Wolfenbüttel Speakers: Prof. Dr. Edgar Wingender, BIOBASE, Wolfenbüttel „Making Sense of Transcriptomics and Proteomics - New Frontiers of Integrative Biology” Dr. Hauke Stephan Busch, German Cancer Research Center – DKFZ – TP3, Heidelberg “CD95-induced Appoptosis: An Example for Large-Scale Modeling of Signal Transduction Networks” Dr. Alexander Kel/ Holger Karas, BIOBASE, Wolfenbüttel „Presentation of the ExPlain System” Organizer: BIOBASE GmbH Date: January, 27 2006 Time: 3 pm – 4:30 pm Duration: ca 1 hour 30 minutes Attendees: 110 - 140 Topic: Cutting-edge Biology for Explaining Expression Data Chair: Alena Kemper, BIOBASE, Wolfenbüttel Speakers: Prof. Dr. Edgar Wingender, BIOBASE, Wolfenbüttel „Making Sense of Transcriptomics and Proteomics - New Frontiers of Integrative Biology” Prof. Dr. Jürgen Borlak, Fraunhofer Institute of Toxicology and Experimental Medicine, Center for Drug Research and Medical Biotechnology, Hannover „Regulatory Networks of Liver-enriched Transcription Factors in Liver Biology and Disease” Dr. Alexander Kel/ Holger Karas , BIOBASE, Wolfenbüttel „Presentation of the ExPlain System” - 111 -
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- 1 - Luxembourg, January 25th to 2
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Table of content PREFACE ..........
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Preface In 1998, we organized the f
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Acknowledgments This meeting has be
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Group B (15h00 - 17h00) Session V.
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- 11 - Exhibition
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Visit our Expo (in alphabetical ord
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Thursday January 26th, 2006 (Early
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Thursday January 26th, 2006 (Evenin
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Regulation of inflammation and gluc
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Saturday January 28th, 2006 (Early
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Oral presentations (by alphabetical
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4: : Lottin S, Vercoutter-Edouart A
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the B-Raf/mitogen-activated/extrace
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Albertini MC, Accorsi A, Citterio B
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AP-1-dependent gene expression in s
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Jaks and cytokine receptors - an in
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The Role of Met-Gab1 Signalling in
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The mammalian tumor suppressor Scri
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SIGNAL TRANSDUCTION BY STRESS-ACTIV
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Title to be announced Caroline Dive
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Mechanisms of DNA methylation in ma
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Blocking the "4 Integrin-Paxillin I
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Regulation of NF-kB-dependent trans
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The immunomodulator AS101 induces g
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Signaling pathways leading to the a
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Boute, N., Jockers, R. and Issad, T
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Jespsen JS, Sorensen MD and Wengel
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8. Nishikawa, H., Kawai, K., Tanaka
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Page 65 and 66: Cross-talk between angiotensin II a
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Page 87 and 88: HOW ANTITOXIC AND ANTICANCER AGENTS
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Page 91 and 92: Epigenetic Regulation of Stem Cell
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Page 95 and 96: Distinct roles of IRF-3 and IRF-7 i
Page 97 and 98: Redox-Sensitive Transcription Facto
Page 99 and 100: Epigenic control of MHC2TA transcri
Page 101 and 102: Attenuation of MSK1-driven NF-kB ge
Page 103 and 104: Talking to chromatin: Silencers Sil
Page 105 and 106: Ubiquitin ligase Smurf1 controls os
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Page 109: Ambion MicroRNAs (miRNAs) are small
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Page 119 and 120: Session I : protein domains Poster
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Page 127 and 128: Session II. Receptor signaling and
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Session II : Receptor signaling and
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Session III. Protein kinase cascade
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Session III : Protein kinase cascad
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Session IV. Protein kinase inhibito
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IV. Protein kinase inhibitors: insi
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IV. Protein kinase inhibitors: insi
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V. Phosphatases as key cell signali
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VI. Proteasome degradation pathways
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VI. Proteasome degradation pathways
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Session VII. Stem cell specific cel
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VIII. Inflammation specific signali
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Session IX. Novel compounds targeti
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Session X : Cell death in cancer -
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Session X : Cell death in cancer Po
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Session XI : Cell death and cardiov
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Session XI: Cell death and cardiova
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Session XII : Cell death and neurod
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Session XIII : Cell signaling pathw
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Session XIV : Transcriptional and t
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Session XV : Reactive oxygen specie
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Session XVI : Chemopreventive agent
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Session XVII : Cell signaling in he
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Dr. Nassera Aouali L-1526 Luxembour
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Dr. Giordano Bianchi Clinic of inte
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Mrs. Isabel Burghardt Laboratory of
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Pr. Czeslaw Cierniewski 92-215 Lodz
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Mr. Igotz Delgado Biochemistry 4894
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Mrs. Anissa Fergani INSERM U-692 67
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Dr. Mark Ginsberg Mail code 0726 92
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Dr. Jochen Hefl Division of Signal
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Mr. Jan Jepsen 2100 Copenhagen DNK
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Pr. Young Min Kim Division of Biolo
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Mr. Christoph Lahtz AG Tumorgenetik
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Pr. Etta Livneh 84105 Beer Sheva IS
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Mrs. Rasa Merzvinskyte Department o
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Mr. Gustav Nilsonne Department of L
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Mrs. Christel Péqueux Tumour and D
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Dr. Gabriella Regis Tumor Immunolog
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Dr. Carsten Scheller 97078 Wuerzbur
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Mr. Yoo-Cheol Song Laboratory of Gy
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Dr. Lucia Maria Valatro Laboratori
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Mrs. Jessica Wagener 40225 Duesseld
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Pr. Moncef ZOUALI Centre Viggo Pete
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