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Repetitive structures in biological sequences are emerging as an active focus of research and the unifying concept of "repeatome" (the ensemble of knowledge associated with repeating structures in genomic/proteomic sequences) has been recently proposed in order to highlight several converging trends. One main trend is the ongoing discovery that genomic repetitions are linked to many biological significant events and functions. Diseases (e.g. Huntington's disease) have been causally linked with abnormal expansion of certain repeating sequences in the human genome. Deletions or multiple copy duplications of genes (Copy Number Variations) are important in the aetiology of cancer, Alzheimer, and Parkinson diseases. A second converging trend has been the emergence of many different models and algorithms for detecting non-obvious repeating patterns in strings with applications to in genomic data. Borrowing methodologies from combinatorial pattern, matching, string algorithms, data structures, data mining and machine learning these new approaches break the limitations of the current approaches and offer a new way to design better trans-disciplinary research. The articles collected in this book provides a glance into the rich emerging area of repeatome research, addressing some of its pressing challenges. We believe that these contributions are valuable resources for repeatome research and will stimulate further research from bioinformatic, statistical, and biological points of view.
Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
This book constitutes the refereed proceedings of the 14th International Conference on Field-Programmable Logic, FPL 2003, held in Leuven, Belgium in August/September 2004. The 78 revised full papers, 45 revised short papers, and 29 poster abstracts presented together with 3 keynote contributions and 3 tutorial summaries were carefully reviewed and selected from 285 papers submitted. The papers are organized in topical sections on organic and biologic computing, security and cryptography, platform-based design, algorithms and architectures, acceleration application, architecture, physical design, arithmetic, multitasking, circuit technology, network processing, testing, applications, signal processing, computational models and compiler, dynamic reconfiguration, networks and optimisation algorithms, system-on-chip, high-speed design, image processing, network-on-chip, power-aware design, IP-based design, co-processing architectures, system level design, physical interconnect, computational models, cryptography and compression, network applications and architecture, and debugging and test.
This textbook presents mathematical models in bioinformatics and describes biological problems that inspire the computer science tools used to manage the enormous data sets involved. The first part of the book covers mathematical and computational methods, with practical applications presented in the second part. The mathematical presentation avoids unnecessary formalism, while remaining clear and precise. The book closes with a thorough bibliography, reaching from classic research results to very recent findings. This volume is suited for a senior undergraduate or graduate course on bioinformatics, with a strong focus on mathematical and computer science background.
This book represents the most comprehensive and up-to-date collection of information on the topic of computational molecular biology. Bringing the most recent research into the forefront of discussion, Algorithms in Computational Molecular Biology studies the most important and useful algorithms currently being used in the field, and provides related problems. It also succeeds where other titles have failed, in offering a wide range of information from the introductory fundamentals right up to the latest, most advanced levels of study.
This book focuses on soft computing and how it can be applied to solve real-world problems arising in various domains, ranging from medicine and healthcare, to supply chain management, image processing and cryptanalysis. It gathers high-quality papers presented at the International Conference on Soft Computing: Theories and Applications (SoCTA 2020), organized online. The book is divided into two volumes and offers valuable insights into soft computing for teachers and researchers alike; the book will inspire further research in this dynamic field.
The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable and the trend is to increase its pace. In fact, the need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology is still increasing driven by new advances in Next Generation Sequencing, several types of the so called omics data and image acquisition, just to name a few. The analysis of the datasets that produces and its integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Within this scenario of increasing data availability, Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘13 hopes to contribute to this effort promoting this fruitful interaction. PACBB'13 technical program included 19 papers from a submission pool of 32 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly have promoted the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work that is being developed by each of the participants.
This book constitutes the refereed proceedings of the International Symposium on Bioinformatics Research and Applications, ISBRA 2012, held in Dallas, Texas, USA, in May 2012. The 26 revised full papers presented together with five invited talks were carefully reviewed and selected from 66 submissions. The papers address issues on various aspects of bioinformatics and computational biology and their applications.
Last, but not least, thanks to all the participants and authors. We hope that they enjoyed the workshop as much as the wonderful and culturally vibrant city of Kolkata! Bhabani P. Sinha Indian Statistical Institute, Kolkata, India December 2004 Sajal K. Das University of Texas, Arlington, USA December 2004 Program Chairs’ Message On behalf of the Technical Program Committee of the 6th International Wo- shop on Distributed Computing, IWDC 2004, it was our great pleasure to w- come the attendees to Kolkata, India. Over the last few years, IWDC has emerged as an internationally renowned forum for interaction among researchers from academia and industries around the world. A clear indicator of this fact is the large number of high-quality submissions of technical papers received by the workshop this year. The workshop program consisted of 12 technical sessions with 54 contributed papers, two keynote addresses, four tutorials, a panel, a poster session and the Prof.A.K.ChoudhuryMemorialLecture.TheIWDCProgramCommittee,c- prising 38 distinguished members, worked hard to organize the technical p- gram. Following a rigorous review process, out of 157 submissions only 54 - pers were accepted for presentation in the technical sessions; 27 of the accepted papers were classi?ed as regular papers and the remaining 27 as short papers. Another 11 papers were accepted for presentation in the poster session, each with a one-page abstract appearing in the proceedings.
String algorithms are a traditional area of study in computer science. In recent years their importance has grown dramatically with the huge increase of electronically stored text and of molecular sequence data (DNA or protein sequences) produced by various genome projects. This book is a general text on computer algorithms for string processing. In addition to pure computer science, the book contains extensive discussions on biological problems that are cast as string problems, and on methods developed to solve them. It emphasises the fundamental ideas and techniques central to today's applications. New approaches to this complex material simplify methods that up to now have been for the specialist alone. With over 400 exercises to reinforce the material and develop additional topics, the book is suitable as a text for graduate or advanced undergraduate students in computer science, computational biology, or bio-informatics. Its discussion of current algorithms and techniques also makes it a reference for professionals.