Computational Cell Biology, 1st ed. 2018 Methods and Protocols Methods in Molecular Biology Series, Vol. 1819

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.

Part I: Big Data- and its Implications in Cell Biology

1. Rule-based Models and Applications in Biology

Álvaro Bustos, Ignacio Fuenzalida1, Rodrigo Santibáñez, Tomás Pérez-Acle, and

2. Optimized Protein-protein Interaction Network usage with Context Filtering

Natalia Pietrosemolia and Maria Pamela Dobay

Part II: Data-driven Analyses of High-throughput Datasets

3. SignaLink: Multi-layered Regulatory Networks

Luca Csabai1, Márton Ölbei, Aidan Budd, Tamás Korcsmáros, and Dávid Fazekas

4. Interplay between Long Non-coding RNAs and microRNAs in Cancer

5. Methods and Tools in Genome-wide Association Studies

Part III: Network-based Modeling of Cellular Phenotypes

6. Identifying Differentially Expressed Genes using Fluorescence-Activated Cell Sorting (FACS) and RNA Sequencing from Low Input Samples

Natalie M Clark, Adam P Fisher, and Rosangela Sozzani

7. Computational and Experimental Approaches to Predict Host-parasite Protein-protein Interactions

Yesid Cuesta-Astroz and  Guilherme Oliveira

8. An Integrative Approach to Virus-host Protein-protein Interactions

Helen V Cook1 and Lars Juhl Jensen

9. The SQUAD Method for the Qualitative Modeling of Regulatory Networks

Akram M´endez , Carlos Ram´ırez, Mauricio P´erez Mart´ınez, and Luis Mendoza

10. miRNet - functional Analysis and Visual Exploration of miRNA-target Interactions in a Network Context

11. Systems Biology Analysis to Understand Regulatory miRNA Networks in Lung Cancer

Meik Kunz, Andreas Pittroff,  and Thomas Dandekar

Part IV: Mathematical Modeling of Cellular Phenotypes

14. Computational Models of Cell Cycle Transitions

15. Simultaneous Profiling of DNA Accessibility and Gene Expression Dynamics with ATAC-Seq and RNA-Seq

David G. Hendrickson, Ilya Soifer, Bernd Wranik, David Botstein, R. Scott McIsaac

16. Computational Network Analysis for Drug Toxicity Prediction

Hardt C, Bauer C, Schuchhardt J, and Herwig R

17. Modeling the Epigenetic Landscape in Plant Development

Davila-Velderrain, Jose, Caldu-Primo, Jose Luis, Martinez-Garcia, Juan Carlos, and Alvarez-Buylla, Elena R.

18. Developing Network Models of Multi-scale Host Responses Involved in Infections and Diseases

Rohith Palli and Juilee Thakar

PART V: Computational Analyses of Heterogenous Cell Populations and Organisms

Margaritis Voliotisa, Kathryn L. Garnerc, Hussah Alobaidc, Krasimira Tsaneva-Atanasovaa, and Craig A. McArdlec

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts