Computational Cell Biology: Methods and Protocols

Front Matter ....Pages i-xi
Front Matter ....Pages 1-1
 Rule-Based Models and Applications in Biology  (Álvaro Bustos, Ignacio Fuenzalida, Rodrigo Santibáñez, Tomás Pérez-Acle, Alberto J. M. Martin)....Pages 3-32
 Optimized Protein–Protein Interaction Network Usage with Context Filtering  (Natalia Pietrosemoli, Maria Pamela Dobay)....Pages 33-50
Front Matter ....Pages 51-51
 SignaLink: Multilayered Regulatory Networks  (Luca Csabai, Márton Ölbei, Aidan Budd, Tamás Korcsmáros, Dávid Fazekas)....Pages 53-73
 Interplay Between Long Noncoding RNAs and MicroRNAs in Cancer  (Francesco Russo, Giulia Fiscon, Federica Conte, Milena Rizzo, Paola Paci, Marco Pellegrini)....Pages 75-92
 Methods and Tools in Genome-wide Association Studies  (Anja C. Gumpinger, Damian Roqueiro, Dominik G. Grimm, Karsten M. Borgwardt)....Pages 93-136
Front Matter ....Pages 137-137
 Identifying Differentially Expressed Genes Using Fluorescence-Activated Cell Sorting (FACS) and RNA Sequencing from Low Input Samples  (Natalie M. Clark, Adam P. Fisher, Rosangela Sozzani)....Pages 139-151
 Computational and Experimental Approaches to Predict Host–Parasite Protein–Protein Interactions  (Yesid Cuesta-Astroz, Guilherme Oliveira)....Pages 153-173
 An Integrative Approach to Virus–Host Protein–Protein Interactions  (Helen V. Cook, Lars Juhl Jensen)....Pages 175-196
 The SQUAD Method for the Qualitative Modeling of Regulatory Networks  (Akram Méndez, Carlos Ramírez, Mauricio Pérez Martínez, Luis Mendoza)....Pages 197-214
 miRNet—Functional Analysis and Visual Exploration of miRNA–Target Interactions in a Network Context  (Yannan Fan, Jianguo Xia)....Pages 215-233
 Systems Biology Analysis to Understand Regulatory miRNA Networks in Lung Cancer  (Meik Kunz, Andreas Pittroff, Thomas Dandekar)....Pages 235-247
 Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks  (Anastasia Baryshnikova)....Pages 249-268
Front Matter ....Pages 269-269
 Toward Large-Scale Computational Prediction of Protein Complexes  (Simone Rizzetto, Attila Csikász-Nagy)....Pages 271-295
 Computational Models of Cell Cycle Transitions  (Rosa Hernansaiz-Ballesteros, Kirsten Jenkins, Attila Csikász-Nagy)....Pages 297-316
 Simultaneous Profiling of DNA Accessibility and Gene Expression Dynamics with ATAC-Seq and RNA-Seq  (David G. Hendrickson, Ilya Soifer, Bernd J. Wranik, David Botstein, R. Scott McIsaac)....Pages 317-333
 Computational Network Analysis for Drug Toxicity Prediction  (C. Hardt, C. Bauer, J. Schuchhardt, R. Herwig)....Pages 335-355
 Modeling the Epigenetic Landscape in Plant Development  (Jose Davila-Velderrain, Jose Luis Caldu-Primo, Juan Carlos Martinez-Garcia, Elena R. Alvarez-Buylla)....Pages 357-383
 Developing Network Models of Multiscale Host Responses Involved in Infections and Diseases  (Rohith Palli, Juilee Thakar)....Pages 385-402
Front Matter ....Pages 403-403
 Exploring Dynamics and Noise in Gonadotropin-Releasing Hormone (GnRH) Signaling  (Margaritis Voliotis, Kathryn L. Garner, Hussah Alobaid, Krasimira Tsaneva-Atanasova, Craig A. McArdle)....Pages 405-429
Back Matter ....Pages 431-436