Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany .... and Cancer Research, Rostock University .... Mohit Kumar Jolly.
Book title: Computational Biology of Non-Coding RNA in Biomedicine Editors: Xin Lai1, Shailendra Gupta2, Julio Vera1 1
Laboratory of Systems Tumour Immunology, Department of Dermatology, Friedrich-Alexander-
University of Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany 2
Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
Series editor: John M. Walker Series: Methods in Molecular Biology (www.springer.com/series/7651) For almost 30 years, biological scientists have come to rely on the research protocols and methodologies in the critically acclaimed Methods in Molecular Biology series. The series was the first to introduce the step-by-step protocols approach that has become the standard in all biomedical protocol publishing. Each protocol is provided in readily-reproducible step-by-step fashion, opening with an introductory overview, a list of the materials and reagents needed to complete the experiment, and followed by a detailed procedure that is supported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitute the key ingredient in each and every volume of the Methods in Molecular Biology series. Tested and trusted, all protocols from the series are indexed in Pub Med, comprehensive and reliable. Publisher: Springer Nature Estimated time for publication: summer 2018
Table of Content Chapter Chapter Titles Article Type Index Part 1. Overview of disease-specific ncRNAs 1 ncRNAs in inflammatory and infectious diseases Review chapter p73-governed miRNA landscape: translating bioinformatics approaches to therapeutic 2 Review chapter solutions for metastasis Part 2. Computational methods and workflows for ncRNA discovery and annotation based on high-throughput sequencing data MiMB format 3 Methods for annotation and validation of circular RNAs from RNAseq data chapter Methods to study long non-coding RNA expression and dynamics in zebrafish using MiMB format 4 RNA sequencing chapter 5 Workflow development strategies for the functional characterization of ncRNAs Review chapter 6 ncRNA editing: functional characterization and computational resources Review chapter 7 Computational prediction of functional microRNA-mRNA interactions Review chapter Part 3. Bioinformatics tools and databases for ncRNA analyses 8 Tools for understanding miRNA-mRNA interactions for reproducible RNA analysis Review chapter Computational resources for identifying functional miRNAs regulation and their 9 Review chapter interactome 10 Non-coding RNAs databases: current status and trends Review chapter Part 4. Network-based methods for characterizing ncRNA function Controllability methods for identifying associations between critical control ncRNAs and 11 Review chapter human diseases Network-based methods and other approaches for predicting lncRNA functions and 12 Review chapter disease associations Integration of miRNA and mRNA expression data for understanding etiology of 13 Review chapter gynecologic cancers Part 5. Kinetic modelling of ncRNA-mediated gene regulation 14 Quantitative characteristics of ncRNA regulation in gene regulatory networks Review chapter Kinetic modelling of competition and depletion of shared miRNAs by competing 15 Review chapter endogenous RNAs 16 Modelling ncRNA-mediated circuits in cell fate decision Review chapter 17 Modeling ncRNA-mediated regulation of the G1 checkpoint in the mammalian cell cycle Review chapter
The list of Authors Authors
Affiliation 1
Affiliation 2
Alan Mitchell Durham
Computer Science Department, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
Alexandre Rossi Paschoal
Department of Computer Science, Bioinformatics Graduation Program (PPGBIOINFO), Universidade Tecnológica Federal do Paraná, Cornélio Procópio, Brazil
Almir José Ferreira
Computer Science Department, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
Ambily Sivadas
G.N. Ramachandran knowledge center for Bioinformatics, CSIR Institute of Genomics and Integrative Biology (CSIRIGIB), Mathura Road, Delhi, India
Andrea Bagnacani
Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Universitätsplatz 1, 18051 Rostock, Germany.
Andrea De Martino
Soft & Living Matter Lab, CNRNANOTEC, Rome, Italy
Italian Institute for Genomic Medicine, via Nizza 52, 10126 Turin, Italy
Andrea Pagnani
DISAT, Politecnico di Torino, corso Duca degli Abruzzi 24, 10129 Turin, Italy
Italian Institute for Genomic Medicine, via Nizza 52, 10126 Turin, Italy
Annalisa Marsico
Institut für Informatik, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany
Max-Planck-Institut für molekulare Genetik, Ihnestraße 63-73, 14195 Berlin, Germany
Araks Martirosyan
Laboratory of Glia Biology, VIB-KU Leuven Center for Brain and Disease Research and KU Leuven Department of Neuroscience, O&N4 Herestraat 49 box 602, 3000 Leuven, Belgium
Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi, India
Bernd Schmeck
Institute for Lung Research, Universities of Giessen and Marburg Lung Center, Philipps-University Marburg, Member of the German Center for Lung Research (DZL), Hans-Meerwein-Str. 2, 35043 Marburg, Germany
Brigitte M. Pützer
Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057, Rostock, Germany
Carla Bosia
DISAT, Politecnico di Torino, corso Duca degli Abruzzi 24, 10129 Turin, Italy
Carlo M. Croce
Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
Chiara Enrico Bena
DISAT, Politecnico di Torino, corso Duca degli Abruzzi 24, 10129 Turin, Italy
Christina Stielow
Institute for Lung Research, Universities of Giessen and Marburg Lung Center, Philipps-University Marburg, Member of the German Center for Lung Research (DZL), Hans-Meerwein-Str. 2, 35043 Marburg, Germany
Dario Veneziano
Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
David Leon Brauer
Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Universitätsplatz 1, 18051 Rostock, Germany.
Disha Sharma
G.N. Ramachandran knowledge center for Bioinformatics, CSIR Institute of Genomics and Integrative Biology (CSIRIGIB), Mathura Road, Delhi, India
Federica Calore
Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
Italian Institute for Genomic Medicine, via Nizza 52, 10126 Turin, Italy
Italian Institute for Genomic Medicine, via Nizza 52, 10126 Turin, Italy
Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi, India
Federico Bocci
Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
Gioacchino P. Marceca
Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
Giovanni Nigita
Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
Giulia Romano
Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
Hanah Goetz
School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287-9709, USA
Herbert Levine
Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
Isha Monga
Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39-A, Chandigarh-160036, India
Jens Allmer
Applied Bioinformatics, Bioscience, Wageningen University & Research, Wageningen, the Netherlands
Jomar F. Rabajante
Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, Laguna 4031, Philippines
Jose C. Nacher
Department of Information Science, Faculty of Science, Toho University, Japan
José Carlos Caris-Maldonado
Advanced Center for Chronic Diseases – ACCDiS, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
José N. Onuchic
Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
Judith Hariprakash
G.N. Ramachandran knowledge center for Bioinformatics, CSIR Institute of Genomics and Integrative Biology (CSIRIGIB), Mathura Road, Delhi, India
Department of Clinical and Experimental Medicine, University of Catania, Catania, CT, 95125, Italy
Kriti Kaushik
Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, India
Leon Schulte
Institute for Lung Research, Universities of Giessen and Marburg Lung Center, Philipps-University Marburg, Member of the German Center for Lung Research (DZL), Hans-Meerwein-Str. 2, 35043 Marburg, Germany
Luisa Tomasello
Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
Malik Yousef
Department of Community Information Systems, Zefat Academic College, Zefat, 13206, Israel
Manoj Kumar
Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39-A, Chandigarh-160036, India
Manuela Vanegas Ferro
School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287-9709, USA
Marco Del Giudice
DISAT, Politecnico di Torino, corso Duca degli Abruzzi 24, 10129 Turin, Italy
Mario Acunzo
Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
Markus Wolfien
Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Universitätsplatz 1, 18051 Rostock, Germany.
Mohit Kumar Jolly
Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
Müşerref Duygu Saçar Demirci
Department of Bioinformatics, Faculty of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi, India
Italian Institute for Genomic Medicine, via Nizza 52, 10126 Turin, Italy
Olaf Wolkenhauer
Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Universitätsplatz 1, 18051 Rostock, Germany.
Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre, University of Stellenbosch, 10 Marais Street, 7600 Stellenbosch, South Africa.
Paras Sehgal
Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, India
Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi, India
Pedro Vinícius Borges
Department of Computer Science, Bioinformatics Graduation Program (PPGBIOINFO), Universidade Tecnológica Federal do Paraná, Cornélio Procópio, Brazil
Ricardo C.H. del Rosario
Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
Rosario Distefano
Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
Rosario Michael Piro
Institut für Informatik, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany
Institut für Medizinische Genetik und Humangenetik, Charite-Universitätsmedizin Berlin, Augusterburger Platz 1, 13353 Berlin, Germany
Samatha Mathew
Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, India
Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhavan, New Delhi 110001, India.
Serge Patrick Nana-Sinkam
Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
Shamsudheen K. Vellarikkal
Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, India
Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi, India
Sridhar Sivasubbu
Stella Logotheti
Stephan Marquardt
G.N. Ramachandran knowledge center for Bioinformatics, CSIR Institute of Genomics and Integrative Biology (CSIRIGIB), Mathura Road, Delhi, India
Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi, India
Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057, Rostock, Germany Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057, Rostock, Germany
Sushmita Paul
Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, India
Tatsuya Akutsu
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan
Vinicius Maracaja-Coutinho
Advanced Center for Chronic Diseases – ACCDiS, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
Vinod Scaria
G.N. Ramachandran knowledge center for Bioinformatics, CSIR Institute of Genomics and Integrative Biology (CSIRIGIB), Mathura Road, Delhi, India
Wilhelm Bertrams
Institute for Lung Research, Universities of Giessen and Marburg Lung Center, Philipps-University Marburg, Member of the German Center for Lung Research (DZL), Hans-Meerwein-Str. 2, 35043 Marburg, Germany
Xiao-Jun Tian
School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287-9709, USA
Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi, India
