Computational Cell Biology

1. Front Matter

   Pages i-xi

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2. Big Data- and Its Implications in Cell Biology

   1. Front Matter

      Pages 1-1

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   2. Rule-Based Models and Applications in Biology

      • Álvaro Bustos, Ignacio Fuenzalida, Rodrigo Santibáñez, Tomás Pérez-Acle, Alberto J. M. Martin

      Pages 3-32

   3. Optimized Protein–Protein Interaction Network Usage with Context Filtering

      • Natalia Pietrosemoli, Maria Pamela Dobay

      Pages 33-50

3. Data-driven Analyses of High-throughput Datasets

   1. Front Matter

      Pages 51-51

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   2. SignaLink: Multilayered Regulatory Networks

      • Luca Csabai, Márton Ölbei, Aidan Budd, Tamás Korcsmáros, Dávid Fazekas

      Pages 53-73

   3. Interplay Between Long Noncoding RNAs and MicroRNAs in Cancer

      • Francesco Russo, Giulia Fiscon, Federica Conte, Milena Rizzo, Paola Paci, Marco Pellegrini

      Pages 75-92

   4. Methods and Tools in Genome-wide Association Studies

      • Anja C. Gumpinger, Damian Roqueiro, Dominik G. Grimm, Karsten M. Borgwardt

      Pages 93-136

4. Network-Based Modeling of Cellular Phenotypes

   1. Front Matter

      Pages 137-137

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   2. 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

   3. Computational and Experimental Approaches to Predict Host–Parasite Protein–Protein Interactions

      • Yesid Cuesta-Astroz, Guilherme Oliveira

      Pages 153-173

   4. An Integrative Approach to Virus–Host Protein–Protein Interactions

      • Helen V. Cook, Lars Juhl Jensen

      Pages 175-196

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

      • Akram Méndez, Carlos Ramírez, Mauricio Pérez Martínez, Luis Mendoza

      Pages 197-214

   6. miRNet—Functional Analysis and Visual Exploration of miRNA–Target Interactions in a Network Context

      • Yannan Fan, Jianguo Xia

      Pages 215-233

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

      • Meik Kunz, Andreas Pittroff, Thomas Dandekar

      Pages 235-247

   8. Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks

      • Anastasia Baryshnikova

      Pages 249-268

5. Mathematical Modeling of Cellular Phenotypes

   1. Front Matter

      Pages 269-269

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   2. Toward Large-Scale Computational Prediction of Protein Complexes

      • Simone Rizzetto, Attila Csikász-Nagy

      Pages 271-295

   3. Computational Models of Cell Cycle Transitions

      • Rosa Hernansaiz-Ballesteros, Kirsten Jenkins, Attila Csikász-Nagy

      Pages 297-316

   4. 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

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.

• high-throughput
• PLS regression
• datasets
• gene-set enrichment
• network inference

“The book recommends itself as an optimal starting point for understanding the current state of the art of data driven analyses, applied on high throughput datasets … . The layout of the chapters makes them accessible to a wide variety of audiences from undergraduates, graduates and established researchers from a wide spectrum of fields from mathematics, computer science to biology and medicine. … this book is a must have for the current research in this field.” (Irina Ioana Mohorianu, zbMATH 1417.92006, 2019)

• NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

  Louise von Stechow

• Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

  Alberto Santos Delgado

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