Encyclopedia of bioinformatics and computational biology Volume 3 Applications
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| 245 | 1 | 0 | |a Encyclopedia of bioinformatics and computational biology |n Volume 3 |p Applications |c editors in chief: Shoba Ranganathan, Macquarie University, Sydney, NSW, Australia, Michael Gribskov, Purdue University, West Lafayette, IN, United States, Kenta Nakai, The University of Tokyo, Tokyo, Japan, Christian Schönbach, Nazarbayev University, School of Science and Technology, Department of Biology, Astana, Kazakhstan |
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| 300 | |a xxiii, 1077 Seiten, Seite 519-524, 848-857 |b Illustrationen, Diagramme | ||
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| 700 | 1 | |a Ranganathan, Shoba |4 edt | |
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| 943 | 1 | |a oai:aleph.bib-bvb.de:BVB01-030621683 | |
Datensatz im Suchindex
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| adam_text | CONTENTS OF VOLUME 3
Editors in Chief v
Volume Editors vii
List of Contributors for Volume 3 xv
Preface xxiii
VOLUME 3
Ecosystem Monitoring Through Predictive Modeling
Sorayya Malek, Cham Hui, Nanyonga Aziida, Song Cheen, Sooh Toh, and Pozi Milow 1
Large Scale Ecological Modeling With Viruses: A Review
Vijayaraghava S Sundararajan 9
Mapping the Environmental Microbiome
Lena Takayasu, Wataru Suda, and Masahira Hatton 17
Biological Database Searching
Nor A Nor Muhammad 29
Extraction of Immune Epitope Information
Guang Lan Zhang, Derin B Keskin, and Lou Chitkushev 39
Characterizing and Functional Assignment of Noncoding RNAs
Pradeep Tiwari, Sonal Gupta, Anuj Kumar, Mansi Sharma, Vijayaraghava S Sundararajan, Shanker
L Kothari, Sandeep K Mathur, Krishna M Medicherla, Babita Malik, and Prashanth Suravajhala 47
Identification and Extraction of Biomarker Information
Vijayaraghava S Sundararajan, Shweta Shrotriya, Monisha Singhal, Pragya Chaturvedi, and
Prashanth Suravajhala 60
Computational Systems Biology Applications
Ayako Yachie-Kinoshita, Sucheendra K Palaniappan, and Samik Ghosh 66
Coupling Cell Division to Metabolic Pathways Through Transcription
Petter Holland, Jens Nielsen, Thierry DGA Mondeel, and Matteo Barberis 74
Studies of Body Systems
Amir Feisal Merican, Hoda Mirsafian, Adiratna Mat Ripen, and Saharuddin Bin Mohamad 94
Host-Pathogen Interactions
Dean Southwood and Shoba Ranganathan 103
Computational Pipelines and Workflows in Bioinformatics
Yosvany Lopez, Piotr J Kamola, Ronesh Sharma, Daichi Shigemizu, Tatsuhiko Tsunoda, and Alok Sharma 113
Constructing Computational Pipelines
ChuangKee Ong and Russell S Hamilton 135
Pipeline of High Throughput Sequencing
ChuangKee Ong, Qi Bin Kwong, Ai Ling Ong, Huey Ying Heng, and Wai Yee Low 144
Genome Annotation: Perspective From Bacterial Genomes
Alan Christoff els and Peter van Heusden 152
IX
x Contents of Volume 3
Next Generation Sequencing Data Analysis
Ranjeev Hari and Suhanya Parthasarathy 157
Exome Sequencing Data Analysis
Anita Sathyanarayanan, Srikanth Manda, Mukta Poojary, and Shivashankar H Nagaraj 164
Whole Genome Sequencing Analysis
Rui Yin, Chee Keong Kwoh, and Jie Zheng 176
Metagenomic Analysis and its Applications
Arpita Ghosh, Aditya Mehta, and Asi/M Khan * 184
Integrative Analysis of Multi-Omics Data
Lokesh P Tripathi, Tsuyoshi Esaki, Mari N Itoh, Yi-An Chen, and Kenji Mizuguchi 194
Profiling the Gut Microbiome: Practice and Potential
Toral Manvar and Vijay lakhujani 200
Functional Enrichment Analysis
Srikanth Manda, Daliah Michael, Sudhir Jadhao, and Shivashankar H Nagaraj 218
Prediction of Coding and Non-Coding RNA
Ranjeev Hari and Suhanya Parthasarathy 230
Vaccine Target Discovery
Li C Chong and Asif M Khan 241
Protocol for Protein Structure Modelling
Amara Jabeen, Abidali Mohamedali, and Shoba Ranganathan 252
Structure-Based Drug Design Workflow
Ari Hardianto, Muhammad Yusuf, Fei Liu, and Shoba Ranganathan 273
Network-Based Analysis for Biological Discovery
Lokesh P Tripathi, Yoichi Murakami, Yi-An Chen, and Kenji Mizuguchi 283
Sequence Analysis
Audrey D Prjibelski, Anton I Korobeynikov, and Alla L Lapidus 292
Sequence Composition
Bryan T Li, Jin Xing Lim, and Maurice HT Ling 323
Codon Usage
Raimi M Redwan, Suhanya Parthasarathy, and Ranjeev Hari 327
Identification of Sequence Patterns, Motifs and Domains
Michael Gribskov 332
Epigenetics: Analysis of Cytosine Modifications at Single Base Resolution
Malwina Prater and Russell S Hamilton 341
Comparative Epigenomics
Yutaka Saito 354
Genetics and Population Analysis
Fotis Tsetsos, Petros Drineas, and Peristera Paschou 363
Population Analysis of Pharmacogenetic Polymorphisms
Zen H Lu, Nani Azman,
Mark 1R Petalcorin, Naeem Shafqat, and Lie Chen 379
Detecting and Annotating Rare Variants
Jieming Chen, Akdes S Harmanci, and Arif O Harmanci
388
Contents of Volume 3 xi
Predicting Non-Synonymous Single Nucleotide Variants Pathogenic Effects in Human Diseases
Marwa S Hassan, AA Shaalan, MI Dessouky, Abdelaziz E Abdelnaiem, Dalia A Abdel-Haleem, and
Mahmoud ElHefnawi 400
Genome Analysis - Identification of Genes Involved in Host-Pathogen Protein-Protein Interaction
Networks
Fransiskus Xaverius Ivan, Jie Zheng, Vincent TK Chow, and Chee-Keong Kwoh 410
Comparative Genomics Analysis
Hui San Ong 425
Single Nucleotide Polymorphism Typing
Srilakshmi Srinivasan and Jyotsna Batra 432
Genome-Wide Haplotype Association Study
Yongshuai Jiang and Jing Xu 441
Prediction of Protein-Binding Sites in DNA Sequences
Kenta Nakai 447
Genome-Wide Scanning of Gene Expression
Sung-J Park 452
Metabolome Analysis
Camila Pereira Braga and Jiri Adamec 463
Disease Biomarker Discovery
Tiratha R Singh, Ankita Shukla, Bensellak Taoufik, Ahmed Moussa, and Brigitte Vannier 476
Investigating Metabolic Pathways and Networks
Md Altaf-Ul-Amin, Zeti-Azura Mohamed-Hussein, and Shigehiko Kanaya 489
Biomolecular Structures: Prediction, Identification and Analyses
Prasun Kumar, Swagata Haider, and Manju Bansal 504
Engineering of Supramolecular RNA Structures
Effirul I Ramlan and Mohd Firdaus-Raih 535
Predicting RNA-RNA Interactions in Three-Dimensional Structures
Hazrina Y Hamdani, Zatil H Yahaya, and Mohd Firdaus-Raih 546
Applications of Ribosomal RNA Sequence and Structure Analysis for Extracting Evolutionary and
Functional Insights
Chyan Leong Ng and Mohd Firdaus-Raih 554
Computational Design and Experimental Implementation of Synthetic Riboswitches and
Riboregulators
Munyati Othman, Siuk M Ng, and Mohd Firdaus-Raih 568
Genome-Wide Probing of RNA Structure
Xiaojing Huo, Jeremy Ng, Mingchen Tan, and
Greg Tucker-Kellogg 574
Assessment of Structure Quality (RNA and Protein)
Nicolas Palopoli 586
Study of the Variability of the Native Protein Structure
Xusi Han, Woong-Hee Shin, Charles W Christoffer, Genki Terashi, Lyman Monroe, and Daisuke Kihara 606
Identifying Functional Relationships Via the Annotation and Comparison of Three-Dimensional
Amino Acid Arrangements in Protein Structures
Mohd Firdaus-Raih and Nur Syatila Abdul Ghani
620
xii Contents of Volume 3
Computational Protein Engineering Approaches for Effective Design of New Molecules
Jaspreet Kaur Dhanjal, Vidhi Malik, Navaneethan Radhakrishnan, Moolchand Sigar, Anjani Kumari, and
Durai Sundar 631
Protein Design
Ragothaman M Yennamalli 644
Molecular Dynamics Simulations in Drug Discovery
Sy-Bing Choi, Beow Keat Yap,
Yee Sieiv Choong, and Habibah Wahab 652
Protein-Carbohydrate Interactions
Adeel Malik, Mohammad H Baig, and Balachandran Manavalan 666
Computational Prediction of Nucleic Acid Binding Residues From Sequence
Nur SA Ghani, Shandar Ahmad, and Mohd Firdaus-Raih 678
Protein-Peptide Interactions in Regulatory Events
Upadhyayula S Raghavender and Ravindranath S Radnore 688
Homologous Protein Detection
Xuefeng Cui and Yaosen Min 697
Mutation Effects on 3D-Structural Reorganization Using HIV-1 Protease as a Case Study
Bistua R Meher, Megha Vaishnavi, Venkata SK Mattaparthi, Seema Patel, and Sandeep Kaushik 706
Structural Genomics
Shuhaila Mat-Sharani, Doris HX Quay, Chyan L Ng, and Mohd Firdaus-Raih 722
Structure-Based Design of Peptide Inhibitors for Protein Arginine Deiminase Type IV (PAD4)
Teo Chian Ying, Zalikha Ibrahim, Mohd Basyaruddin Abd Rahman, and Bimo A Tejo 729
Small Molecule Drug Design
Vartika Tomar, Mohit Mazumder, Ramesh Chandra, Jian Yang, and Meena K Sakharkar 741
In Silico Identification of Novel Inhibitors
Beow Keat Yap, Chong-Yeiv lee, Sy Bing Choi, Ezatul E Kamarulzaman, Maywan Hariono, and Habibah
A Wahab 761
Drug Repurposing and Multi-Target Therapies
Ammu P Kumar, Minh N Nguyen, and Suryani Lukman 780
Transcriptome Analysis
Anuj Srivastava, Joshy George, and Radha KM Karuturi 792
Regulation of Gene Expression
Y-h Taguchi 806
Comparative Transcriptomics Analysis
Y-h Taguchi 814
Analyzing Transcriptome-Phenotype Correlations
Bryan T Li, Jin X Lim, and Maurice HT Ling 819
Transcriptome During Cell Differentiation
Dwi A Pujianto 825
Characterization of Transcriptional Activities
Adison Wong and Maurice HT Ling 830
Survey of Antisense Transcription
Maurice HT Ling 842
Statistical and Probabilistic Approaches to Predict Protein Abundance
Rubbiya A AH, Ali Naqi, Sarah Ali, Mashal Fatima, Musarat Ishaq, and Ahmed M Mehdi
847
Contents of Volume 3 xiii
Identification of Proteins From Proteomic Analysis
Zainab Noor, Abidali Mohamedali, and Shoba Ranganathan 855
Quantification of Proteins From Proteomic Analysis
Zainab Noor, Subash Adhikari, Shoba Ranganathan, and Abidali Mohamedali 871
Utilising IPG-IEF to Identify Differentially-Expressed Proteins
David I Cantor and Harish R Cheruku 891
Clinical Proteomics
Marwenie F Petalcorin, Naeem Shafcjat, Zen H Lu, and Mark IR Petalcorin 911
Molecular Mechanisms Responsible for Drug Resistance
Mun Fai Loke and Aimi Hanafi 926
Network-Based Analysis of Host-Pathogen Interactions
Lokesh P Tripathi, Eiji Morita, Yi-An Chen, and Kenji Mizuguchi 932
Phylogenetic Analysis: Early Evolution of Life
Himakshi Sarma, Sushmita Pradhan, Sandeep Kaushik, and Venkata SK Mattaparthi 938
Inference of Horizontal Gene Transfer: Gaining Insights Into Evolution via Lateral Acquisition of
Genetic Material
Suhaila Sulaiman, Nur S Yusoff, Ng S Mm, Haslina Makmur, and Mohd Firdaus-Raih 953
Gene Duplication and Speciation
Tiratha R Singh and Ankush Bansal 965
Epidemiology: A Review
Vijayaraghava S Sundararajan 975
Identification of Homologs
William R Pearson 980
DNA Barcoding: Bioinformatics Workflows for Beginners
John-James Wilson, Kong-Wah Sing, and Narong Jaturas 985
Text Mining Applications
Raul Rodrigaez-Esteban 996
Index 1001
|
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| author2 | Khan, Mohammad Asif Ranganathan, Shoba Gribskov, Michael Nakai, Kenta |
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| title | Encyclopedia of bioinformatics and computational biology |
| title_auth | Encyclopedia of bioinformatics and computational biology |
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| title_full | Encyclopedia of bioinformatics and computational biology Volume 3 Applications editors in chief: Shoba Ranganathan, Macquarie University, Sydney, NSW, Australia, Michael Gribskov, Purdue University, West Lafayette, IN, United States, Kenta Nakai, The University of Tokyo, Tokyo, Japan, Christian Schönbach, Nazarbayev University, School of Science and Technology, Department of Biology, Astana, Kazakhstan |
| title_fullStr | Encyclopedia of bioinformatics and computational biology Volume 3 Applications editors in chief: Shoba Ranganathan, Macquarie University, Sydney, NSW, Australia, Michael Gribskov, Purdue University, West Lafayette, IN, United States, Kenta Nakai, The University of Tokyo, Tokyo, Japan, Christian Schönbach, Nazarbayev University, School of Science and Technology, Department of Biology, Astana, Kazakhstan |
| title_full_unstemmed | Encyclopedia of bioinformatics and computational biology Volume 3 Applications editors in chief: Shoba Ranganathan, Macquarie University, Sydney, NSW, Australia, Michael Gribskov, Purdue University, West Lafayette, IN, United States, Kenta Nakai, The University of Tokyo, Tokyo, Japan, Christian Schönbach, Nazarbayev University, School of Science and Technology, Department of Biology, Astana, Kazakhstan |
| title_short | Encyclopedia of bioinformatics and computational biology |
| title_sort | encyclopedia of bioinformatics and computational biology applications |
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