Computational Cell Biology: Methods and Protocols

✍ Scribed by Louise von Stechow, Alberto Santos Delgado

• Publisher: Springer New York,Humana Press
• Year: 2018
• Tongue: English
• Leaves: 431
• Series: Methods in Molecular Biology 1819
• Edition: 1st ed.
• Category: Library

✦ Synopsis

This volume details computational techniques for analyses of a wide range of biological contexts, providing an overview of the most up-to-date techniques used in the field. Chapters guide the reader through available data resources and analysis methods and easy-to-follow protocols that allow the researcher to apply various computational tools to an array of different data types. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory and computational protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Computational Cell Biology: Method and Protocols aims to ensure successful results in the further study of this vital field.

✦ Table of Contents

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

✦ Subjects

Life Sciences; Bioinformatics