Biological networks and pathway analysis

Front Matter ....Pages i-xiv
 A Practical Guide to Quantitative Interactor Screening with Next-Generation Sequencing (QIS-Seq)  (Yunchen Gong, Darrell Desveaux, David S. Guttman, Jennifer D. Lewis)....Pages 1-20
 sbv IMPROVER: Modern Approach to Systems Biology  (Svetlana Guryanova, Anna Guryanova)....Pages 21-29
 Mathematical Justification of Expression-Based Pathway Activation Scoring (PAS)  (Alexander M. Aliper, Michael B. Korzinkin, Natalia B. Kuzmina, Alexander A. Zenin, Larisa S. Venkova, Philip Yu. Smirnov et al.)....Pages 31-51
 Bioinformatics Meets Biomedicine: OncoFinder, a Quantitative Approach for Interrogating Molecular Pathways Using Gene Expression Data  (Anton A. Buzdin, Vladimir Prassolov, Alex A. Zhavoronkov, Nikolay M. Borisov)....Pages 53-83
 Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks  (Mark D’Souza, Dinanath Sulakhe, Sheng Wang, Bing Xie, Somaye Hashemifar, Andrew Taylor et al.)....Pages 85-99
 Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated “Knowledge-Based” Platform  (Alexey Dubovenko, Yuri Nikolsky, Eugene Rakhmatulin, Tatiana Nikolskaya)....Pages 101-124
 Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond  (Galina Glazko, Yasir Rahmatallah, Boris Zybailov, Frank Emmert-Streib)....Pages 125-159
 Search for Master Regulators in Walking Cancer Pathways  (Alexander E. Kel)....Pages 161-191
 Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles  (Vladimir A. Kuznetsov)....Pages 193-276
 A Weighted SNP Correlation Network Method for Estimating Polygenic Risk Scores  (Morgan E. Levine, Peter Langfelder, Steve Horvath)....Pages 277-290
 Analysis of cis-Regulatory Elements in Gene Co-expression Networks in Cancer  (Martin Triska, Alexander Ivliev, Yuri Nikolsky, Tatiana V. Tatarinova)....Pages 291-310
 Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways  (Rabie Saidi, Imane Boudellioua, Maria J. Martin, Victor Solovyev)....Pages 311-331
 ArrayTrack: An FDA and Public Genomic Tool  (Hong Fang, Stephen C. Harris, Zhenjiang Su, Minjun Chen, Feng Qian, Leming Shi et al.)....Pages 333-353
 Identification of Transcriptional Regulators of Psoriasis from RNA-Seq Experiments  (Alena Zolotarenko, Evgeny Chekalin, Rohini Mehta, Ancha Baranova, Tatiana V. Tatarinova, Sergey Bruskin)....Pages 355-370
 Comprehensive Analyses of Tissue-Specific Networks with Implications to Psychiatric Diseases  (Guan Ning Lin, Roser Corominas, Hyun-Jun Nam, Jorge Urresti, Lilia M. Iakoucheva)....Pages 371-402
 Semantic Data Integration and Knowledge Management to Represent Biological Network Associations  (Sascha Losko, Klaus Heumann)....Pages 403-423
 Knowledge-Based Compact Disease Models: A Rapid Path from High-Throughput Data to Understanding Causative Mechanisms for a Complex Disease  (Anatoly Mayburd, Ancha Baranova)....Pages 425-461
 Pharmacologic Manipulation of Wnt Signaling and Cancer Stem Cells  (Yann Duchartre, Yong-Mi Kim, Michael Kahn)....Pages 463-478
 Functional Network Disruptions in Schizophrenia  (Irina Rish, Guillermo A. Cecchi)....Pages 479-504
Back Matter ....Pages 505-509