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Encyclopedia of Bioinformatics and Computational Biology 2019

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Shoba Ranganathan, Michael Gribskov, Kenta Nakai, Christian Schönbach:
Encyclopedia of Bioinformatics and Computational Biology - Volume 2. Elsevier 2019, ISBN 978-0-12-811432-2
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Pascale Gaudet:
The Gene Ontology. 1-7
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Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio:
Protein Functional Annotation. 8-14
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Chi N. I. Pang, Marc R. Wilkins:
Protein Post-Translational Modification Prediction. 15-27
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Kentaro Tomii:
Protein Properties. 28-33
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Teresa K. Attwood, Alex L. Mitchell:
The Evolution of Protein Family Databases. 34-45
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Pier Luigi Martelli, Castrense Savojardo, Giuseppe Profiti, Rita Casadio:
Transmembrane Domain Prediction. 46-52
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Kenta Nakai, Kenichiro Imai:
Prediction of Protein Localization. 53-59
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Frédérique Lisacek:
Proteome Informatics. 60-75
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Thibault Robin:
Proteomics Data Representation and Databases. 76-83
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Aivett Bilbao:
Proteomics Mass Spectrometry Data Analysis Tools. 84-95
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Sarinder Kaur Dhillon:
Biological Databases. 96-117
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Shalini Kaushik, Sandeep Kaushik, Deepak Sharma:
Functional Genomics. 118-133
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Edgar Wingender, Alexander E. Kel, Mathias Krull:
Transcription Factor Databases. 134-141
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Preeti Pandey, Sabeeha Hasnain, Shandar Ahmad:
Protein-DNA Interactions. 142-154
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Enze Liu, Lang Li, Lijun Cheng:
Gene Regulatory Network Review. 155-164
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Xiangying Sun, Michael Gribskov:
MicroRNA and lncRNA Databases and Analysis. 165-170
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Molly A. Hall, Brian S. Cole, Jason H. Moore:
Gene-Gene Interactions: An Essential Component to Modeling Complexity for Precision Medicine. 171-177
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Anil K. Kesarwani, Ankit Malhotra, Anuj Srivastava, Guruprasad Ananda, Haitham Ashoor, Parveen Kumar, Rupesh K. Kesharwani, Vishal Kumar Sarsani, Yi Li, Joshy George, Krishna M. Karuturi:
Genome Informatics. 178-194
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Josep F. Abril, Sergi Castellano:
Genome Annotation. 195-209
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Emmanuelle Lerat:
Repeat in Genomes: How and Why You Should Consider Them in Genome Analyses? 210-220
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Prasoon Kumar Thakur, Hukam C. Rawal, Mina Obuca, Sandeep Kaushik:
Bioinformatics Approaches for Studying Alternative Splicing. 221-234
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William S. Bush:
Genome-Wide Association Studies. 235-241
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Kelly L. Williams:
Gene Mapping. 242-250
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Dean Southwood, Shoba Ranganathan:
Genome Databases and Browsers. 251-256
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Takeshi Kawashima:
Comparative and Evolutionary Genomics. 257-267
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Tetsushi Yada:
Genome Alignment. 268-283
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Hiroyuki Toh:
Phylogenetic Footprinting. 284-287
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Wayne K. Dawson, Michal Lazniewski, Dariusz Plewczynski:
Chromatin: A Semi-Structured Polymer. 288-307
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Vladimir B. Teif, Christopher T. Clarkson:
Nucleosome Positioning. 308-317
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Wing-Kin Sung:
Learning Chromatin Interaction Using Hi-C Datasets. 318-323
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Liang Chen, Garry Wong:
Transcriptome Informatics. 324-340
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Askhat Molkenov, Altyn Zhelambayeva, Akbar Yermekov, Saule Mussurova, Aliya Sarkytbayeva, Yerbol Kalykhbergenov, Zhaxybay Zhumadilov, Ulykbek Kairov:
Transcriptomic Databases. 341-351
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Christian Rockmann, Christoph Endrullat, Marcus Frohme, Heike Pospisil:
Next Generation Sequence Analysis. 352-363
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Fatemeh Vafaee, Hamed Dashti, Hamid Alinejad-Rokny:
Transcriptomic Data Normalization. 364-371
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Marc Delord:
Differential Expression From Microarray and RNA-seq Experiments. 372-387
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Xiaoxin Ye, Joshua W. K. Ho:
Expression Clustering. 388-395
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Saravanan Dayalan, Jianguo Xia, Rachel A. Spicer, Reza M. Salek, Ute Roessner:
Metabolome Analysis. 396-409
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Russell Pickford:
Mass Spectrometry-Based Metabolomic Analysis. 410-425
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Joram M. Posma:
Metabolic Profiling. 426-437
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Jean-Marc Schwartz, Zita Soons:
Metabolic Models. 438-444
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M. Michael Gromiha, Raju Nagarajan, Samuel Selvaraj:
Protein Structural Bioinformatics: An Overview. 445-459
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David R. Armstrong, John M. Berrisford, Matthew J. Conroy, Alice R. Clark, Deepti Gupta, Abhik Mukhopadhyay:
Protein Structure Databases. 460-471
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Natalie L. Dawson, Sayoni Das, Jonathan G. Lees, Christine A. Orengo:
Protein Structure Classification. 472-487
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Jonas Reeb, Burkhard Rost:
Secondary Structure Prediction. 488-496
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Sanne Abeln, K. Anton Feenstra, Jaap Heringa:
Protein Three-Dimensional Structure Prediction. 497-511
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Tsuyoshi Shirai:
Protein Structure Analysis and Validation. 512-519
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Sandeep Kaushik, Soumya Lipsa Rath:
Protein Structure Visualization. 520-538
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Luciano A. Abriata:
Computational Tools for Structural Analysis of Proteins. 539-549
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Liangzhen Zheng, Amr Alhossary, Chee-Keong Kwoh, Yuguang Mu:
Molecular Dynamics and Simulation. 550-566
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Airy Sanjeev, Mattaparthi Venkata Satish Kumar, Sandeep Kaushik:
Nucleic-Acid Structure Database. 567-574
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Junichi Iwakiri, Kiyoshi Asai:
RNA Structure Prediction. 575-584
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Varun Khanna, Shoba Ranganathan, Nikolai Petrovsky:
Rational Structure-Based Drug Design. 585-600
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Jaroslaw Polanski:
Chemoinformatics: From Chemical Art to Chemistry in Silico. 601-618
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Daniela Schuster:
Fingerprints and Pharmacophores. 619-627
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Sunghwan Kim:
Public Chemical Databases. 628-639
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Oliver Koch, Nils M. Kriege, Lina Humbeck:
Chemical Similarity and Substructure Searches. 640-649
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Oliver Koch, Christiane Ehrt, Tobias Brinkjost:
Binding Site Comparison - Software and Applications. 650-660
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Swathik Clarancia Peter, Jaspreet Kaur Dhanjal, Vidhi Malik, Navaneethan Radhakrishnan, Mannu Jayakanthan, Durai Sundar:
Quantitative Structure-Activity Relationship (QSAR): Modeling Approaches to Biological Applications. 661-676
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Balakumar Chandrasekaran, Nikhil Agrawal, Sandeep Kaushik:
Pharmacophore Development. 677-687
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Muhammad Yusuf, Ari Hardianto, Muchtaridi Muchtaridi, Rina F. Nuwarda, Toto Subroto:
Introduction of Docking-Based Virtual Screening Workflow Using Desktop Personal Computer. 688-699
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Michael A. Charleston:
Molecular Phylogenetics. 700-711
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David A. Liberles, Barbara R. Holland:
Evolutionary Models. 712-718
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Cara Van Der Wal, Simon Y. W. Ho:
Molecular Clock. 719-726
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Richard J. Edwards:
Phylogenetic Tree Rooting. 727-735
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Mahendra Mariadassou, Avner Bar-Hen, Hirohisa Kishino:
Tree Evaluation and Robustness Testing. 736-745
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Miguel Arenas:
Applications of the Coalescent for the Evolutionary Analysis of Genetic Data. 746-758
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Conrad J. Burden:
Population Genetics. 759-788
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Sucheendra K. Palaniappan, Ayako Yachie-Kinoshita, Samik Ghosh:
Computational Systems Biology. 789-795
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Sarita Poonia, Smriti Chawla, Sandeep Kaushik, Debarka Sengupta:
Pathway Informatics. 796-804
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Paolo Tieri, Lorenzo Farina, Manuela Petti, Laura Astolfi, Paola Paci, Filippo Castiglione:
Network Inference and Reconstruction in Bioinformatics. 805-813
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Laurentino Quiroga Moreno:
Graphlets and Motifs in Biological Networks. 814-820
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Edson Luiz Folador, Sandeep Tiwari, Camila E. Da Paz Barbosa, Syed B. Jamal, Marco Da Costa Schulze, Debmalya Barh, Vasco Ariston de Carvalho Azevedo:
Protein-Protein Interactions: An Overview. 821-833
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Anna Laddach, Sun Sook Chung, Franca Fraternali:
Prediction of Protein-Protein Interactions: Looking Through the Kaleidoscope. 834-848
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Ashwini Patil:
Protein-Protein Interaction Databases. 849-855
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Zhongming Zhao, Junfeng Xia:
Computational Approaches for Modeling Signal Transduction Networks. 856-863
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Ayako Yachie-Kinoshita, Kazunari Kaizu:
Cell Modeling and Simulation. 864-873
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Filippo Castiglione, Emiliano Mancini, Marco Pedicini, Abdul Salam Jarrah:
Quantitative Modelling Approaches. 874-883
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Martin Golebiewski:
Data Formats for Systems Biology and Quantitative Modeling. 884-893
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Josch Pauling:
Computational Lipidomics. 894-899
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Socrates Dokos:
Multi-Scale Modelling in Biology. 900-905
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Marta Gomez-Perosanz, Giulia Russo, Jose Luis Sanchez-Trincado Lopez, Marzio Pennisi, Pedro A. Reche, Adrian J. Shepherd, Francesco Pappalardo:
Computational Immunogenetics. 906-930
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Christine L. P. Eng, Tin Wee Tan, Joo Chuan Tong:
Immunoinformatics Databases. 931-939
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Katherine J. L. Jackson:
Study of Human Antibody Responses From Analysis of Immunoglobulin Gene Sequences. 940-951
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Roman Kogay, Christian Schönbach:
Epitope Predictions. 952-971
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Pazit Polak, Ramit Mehr, Gur Yaari:
Immunoglobulin Clonotype and Ontogeny Inference. 972-983
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Shoya Iwanami, Shingo Iwami:
Quantitative Immunology by Data Analysis Using Mathematical Models. 984-992
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Sorayya Malek, Mogeeb A. A. Mosleh, Sarinder Kaur Dhillon, Pozi Milow:
Bioimage Informatics. 993-1010
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Arpah Abu, Sarinder Kaur Dhillon:
Bioimage Databases. 1011-1027
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Saowaluck Kaewkamnerd, Apichart Intarapanich, Sissades Tongsima:
Segmentation Techniques for Bioimages. 1028-1045
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Sandeep Kaushik, Chakrawarti Prasun, Deepak Sharma:
Translational and Disease Bioinformatics. 1046-1057
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Onkar Singh, Nai-Wen Chang, Hong-Jie Dai, Jitendra Jonnagaddala:
Translational Bioinformatics Databases. 1058-1062
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Hong Yung Yip, Nur Aishah Taib, Haris A. Khan, Sarinder Kaur Dhillon:
Electronic Health Record Integration. 1063-1076
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Madhu Goyal:
Genome Databases and Browsers for Cancer. 1077-1082
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Sandeep Kaushik, Priyanka Baloni, Charu K. Midha:
Text Mining Resources for Bioinformatics. 1083-1092
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Meena K. Sakharkar, Karthic Rajamanickam, Chidambaram S. Babu, Jitender Madan, Ramesh Chandra, Jian Yang:
Preclinical: Drug Target Identification and Validation in Human. 1093-1098
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Hagit Shatkay:
Biomedical Text Mining. 1099-1109
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Lina A. M. Zalani, Kho S. Jye, Shaarmini Balakrishnan, Sarinder Kaur Dhillon:
Biodiversity Databases and Tools. 1110-1123
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Mohammed N. M. Ali, Amy Y. Then Hui, Sarinder Kaur Dhillon:
Challenges in Creating Online Biodiversity Repositories With Taxonomic Classification. 1124-1130
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Kazuhiro Takemoto, Midori Iida:
Ecological Networks. 1131-1141
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Bertil Schmidt, Andreas Hildebrandt:
Dedicated Bioinformatics Analysis Hardware. 1142-1150
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Jeremy Leipzig:
Computational Pipelines and Workflows in Bioinformatics. 1151-1162

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