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| clc genomics workbench rna seq analysis: Bioinformatics David Edwards, Jason Stajich, David Hansen, 2010-04-29 Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory. The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding. |
| clc genomics workbench rna seq analysis: Bioinformatics in Aquaculture Zhanjiang (John) Liu, 2017-04-17 Bioinformatics derives knowledge from computer analysis of biological data. In particular, genomic and transcriptomic datasets are processed, analysed and, whenever possible, associated with experimental results from various sources, to draw structural, organizational, and functional information relevant to biology. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics in Aquaculture provides the most up to date reviews of next generation sequencing technologies, their applications in aquaculture, and principles and methodologies for the analysis of genomic and transcriptomic large datasets using bioinformatic methods, algorithm, and databases. The book is unique in providing guidance for the best software packages suitable for various analysis, providing detailed examples of using bioinformatic software and command lines in the context of real world experiments. This book is a vital tool for all those working in genomics, molecular biology, biochemistry and genetics related to aquaculture, and computational and biological sciences. |
| clc genomics workbench rna seq analysis: Applications of RNA-Seq and Omics Strategies Fabio Marchi, Priscila Cirillo, Elvis Cueva Mateo, 2017-09-13 The large potential of RNA sequencing and other omics techniques has contributed to the production of a huge amount of data pursuing to answer many different questions that surround the science's great unknowns. This book presents an overview about powerful and cost-efficient methods for a comprehensive analysis of RNA-Seq data, introducing and revising advanced concepts in data analysis using the most current algorithms. A holistic view about the entire context where transcriptome is inserted is also discussed here encompassing biological areas with remarkable technological advances in the study of systems biology, from microorganisms to precision medicine. |
| clc genomics workbench rna seq analysis: 6th International Conference on Practical Applications of Computational Biology & Bioinformatics Miguel P. Rocha, Nicholas Luscombe, Florentino Fdez-Riverola, Juan M. Corchado Rodríguez, 2012-03-05 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‘12 hopes to contribute to this effort promoting this fruitful interaction. PACBB'12 technical program included 32 papers from a submission pool of 61 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. |
| clc genomics workbench rna seq analysis: Identifying Clinically Relevant Transcriptional Signatures and Methylation Profiles in the Course, Treatment and Outcome of Colorectal Cancer Zora Lasabova, Pooneh Mokarram, Martina Poturnajova, Mozhdeh Zamani, 2024-03-28 Despite major efforts to stratify colorectal cancer patients, only a few prognostic and predictive biomarkers are still used in clinical practice. Inter- and intratumoral heterogeneity is one of the factors influencing strategies for biomarker identification and their implementation in clinical decisions. Recent characterization of consensus molecular subtypes has demonstrated the importance of transcriptome analysis, but the need for in-depth analysis considering other parameters has become apparent. Strategies to study and understand inter- and intratumoral heterogeneity at the tumor tissue level, focusing on gene expression, transcriptomics, and epigenetics, may improve colorectal cancer classification and lead to the identification of biomarkers of prognostic and predictive importance to complement genetics. They could lead to a better understanding of the causes of treatment failure and disease recurrence and thus to new possibilities for patient stratification. Liquid biopsy is currently an effective strategy to capture tumor heterogeneity in non-invasive monitoring of disease progression and recurrence. |
| clc genomics workbench rna seq analysis: Halophytes for Food Security in Dry Lands Muhammad Ajmal Khan, Munir Ozturk, Bilquees Gul, Muhammad Zaheer Ahmed, 2015-09-15 Halophytes for Food Security in Dry Lands addresses the concerns surrounding global food scarcity, especially focusing on those living in arid and dry lands The book touches on food crises in dry regions of the world and proposes halophytes as an alternate source of consumption for such areas. Halophytes, those plants that thrive in saline soil and provide either food source options themselves, or positively enhance an eco-system's ability to produce food, and are thus an important and increasingly recognized option for addressing the needs of the nearly 1/6 of the world's population that lives in these arid and semi-arid climates. Including presentations from the 2014 International Conference on Halophytes for Food Security in Dry Lands, this book features insights from the leading researchers in the subject. It is a valuable resource that includes information on the nutritional value of halophytes, their genetic basis and potential enhancement, adaption of halophytes, and lessons learned thus far. - Provides comprehensive coverage of the importance and utilization of halophytes to compensate the demand of food in whole world especially in the dry regions - Contains insights from ecological to molecular fields - Includes edible halophytes as well as those that enhance food-producing eco-systems - Presents information for improving abiotic stress tolerance in plants |
| clc genomics workbench rna seq analysis: Bioinformatics and Biomedical Engineering Ignacio Rojas, Olga Valenzuela, Fernando Rojas, Francisco Ortuño, 2019-04-30 The two-volume set LNBI 11465 and LNBI 11466 constitutes the proceedings of the 7th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2019, held in Granada, Spain, in May 2019. The total of 97 papers presented in the proceedings, was carefully reviewed and selected from 301 submissions. The papers are organized in topical sections as follows: Part I: High-throughput genomics: bioinformatics tools and medical applications; omics data acquisition, processing, and analysis; bioinformatics approaches for analyzing cancer sequencing data; next generation sequencing and sequence analysis; structural bioinformatics and function; telemedicine for smart homes and remote monitoring; clustering and analysis of biological sequences with optimization algorithms; and computational approaches for drug repurposing and personalized medicine. Part II: Bioinformatics for healthcare and diseases; computational genomics/proteomics; computational systems for modelling biological processes; biomedical engineering; biomedical image analysis; and biomedicine and e-health. |
| clc genomics workbench rna seq analysis: The Cochlea Peter Dallos, Richard R. Fay, 2012-12-06 Knowledge about the structure and function of the inner ear is vital to an understanding of vertebrate hearing. This volume presents a detailed overview of the mammalian cochlea from its anatomy and physiology to its biophysics and biochemistry. The nine review chapters, written by internationally distinguished auditory researchers, provide a detailed and unified introduction to sound processing in the cochlea and the steps by which the ensuing signals are prepared for the central nervous system. |
| clc genomics workbench rna seq analysis: Gene Expression Analysis Nalini Raghavachari, Natàlia Garcia-Reyero, 2018-05-17 This volume provides experimental and bioinformatics approaches related to different aspects of gene expression analysis. Divided in three sections chapters detail wet-lab protocols, bioinformatics approaches, single-cell gene expression, highly multiplexed amplicon sequencing, multi-omics techniques, and targeted sequencing. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Gene Expression Analysis: Methods and Protocols aims provide useful information to researchers worldwide. |
| clc genomics workbench rna seq analysis: Next-Generation Sequencing Data Analysis Xinkun Wang, 2016-04-06 A Practical Guide to the Highly Dynamic Area of Massively Parallel SequencingThe development of genome and transcriptome sequencing technologies has led to a paradigm shift in life science research and disease diagnosis and prevention. Scientists are now able to see how human diseases and phenotypic changes are connected to DNA mutation, polymorphi |
| clc genomics workbench rna seq analysis: Genomic, Proteomics, and Biotechnology RC Sobti, Manishi Mukesh, Aastha Sobti, 2022-12-29 High-throughput molecular technologies (omics) can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways thereby allowing the discovery of biomarkers. Notably, the omics technologies along with and computational methods, bioprospecting, and artificial intelligence will continue to lead to better understanding of biological mechanisms that are responsible for physical attributes, or phenotypes. Research breakthroughs obtained through these technologies can be used to enhance productivity of food animals, meet the increasing demand for animal-sourced foods, enhance high-quality nutrient availability, ensure nutrient safety, mitigate the effects of climate variability, and result in new technologies that provide continued improvement in food security worldwide. Such breakthroughs are an urgent necessity because over the past 50 years, there has been an unprecedented increase in the world’s population, which will reach ten billion by the year 2050. Innovative and technological advancements that enhance all aspects of food production will arise from basic, fundamental research. Besides food, animal by-products have found many applications in the fields of pharmaceuticals, cosmetics, and household and industrial products. Hence, the need to ameliorate the productivity, reproductivity, growth performance, and disease resistance in animals has created a worldwide interest in gaining a deeper understanding of animal biology, biotechnology and genomics, and proteomics. The present volume thoroughly discusses the omics studies in domestic and non-domestic animals and their role in mitigation of various challenges ahead. The volume thus focuses on i. Omics (genomics, proteomics, transcriptomics, metabolonomics) technologies in identifying, characterizing biodiversity ii. Role of molecular techniques for improvement of domestic and non-domestic organisms iii. Animal and alternative model systems (using stem cells, tissue engineering, cell free systems, 3D platforms etc.) for studying life phenomena iv. Genetically modified organisms as factories for the products |
| clc genomics workbench rna seq analysis: Cereal Genomics Robert J. Henry, Agnelo Furtado, 2013-11-16 In Cereal Genomics: Methods and Protocols, expert researchers provides modern protocols for the analysis and manipulation of cereal genomes. Techniques for isolation and analysis of DNA and RNA from both the vegetative tissues and from the more challenging seeds of cereals are described. Tools for the isolation, characterization and functional analysis of cereal genes and their transcripts are detailed. Methods for molecular screening of cereals and for their genetic transformation are also covered. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Cereal Genomics: Methods and Protocols provides a comprehensive resource for those studying cereal genomes. |
| clc genomics workbench rna seq analysis: Towards a New 3Rs Era in Experimental Research Christopher R. Cederroth, Marta L. Alves Da Silva, Annemarie Lang, Armand Mensen, Peter Bollen, Benjamin Victor Ineichen, Doris Wilflingseder, Jenny Stina-Maria Sandström, Serban Morosan, 2024-04-29 With the persisting need of animal experimentation for fundamental and applied research, the relevance and importance of the 3Rs Principle cannot be ignored. The 3Rs Principle was put forward over 50 years ago, providing an essential framework for more humane animal experimentation in research. In this half-century the research landscape within which this principle is applied has dramatically changed and evolved, with ever more emerging venues to explore for 3Rs advancement and implementation. |
| clc genomics workbench rna seq analysis: Bioinformatics in Aquaculture Zhanjiang (John) Liu, 2017-01-30 Bioinformatics derives knowledge from computer analysis of biological data. In particular, genomic and transcriptomic datasets are processed, analysed and, whenever possible, associated with experimental results from various sources, to draw structural, organizational, and functional information relevant to biology. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics in Aquaculture provides the most up to date reviews of next generation sequencing technologies, their applications in aquaculture, and principles and methodologies for the analysis of genomic and transcriptomic large datasets using bioinformatic methods, algorithm, and databases. The book is unique in providing guidance for the best software packages suitable for various analysis, providing detailed examples of using bioinformatic software and command lines in the context of real world experiments. This book is a vital tool for all those working in genomics, molecular biology, biochemistry and genetics related to aquaculture, and computational and biological sciences. |
| clc genomics workbench rna seq analysis: Next-Generation Sequencing and CRISPR-Cas Editing in Plant Virology Ahmed Hadidi, Henryk Hanokh Czosnek, John Wesley Randles, 2021-11-26 |
| clc genomics workbench rna seq analysis: Molecular and Cellular Mechanisms of the Legume-Rhizobia Symbiosis Jianping Wang, Stig Uggerhøj Andersen, Pascal Ratet, 2019-02-19 The legume-rhizobia symbiosis is a remarkable biological phenomena, which is critically important for sustainable agriculture. In the past decades, significant progress has been made to understand the mechanisms of the symbiotic processes. In this eBook, we present the most recent researches focusing on the molecular mechanisms of legume-rhizobia symbiosis including rhizobium characters, plant response to different types of bacteria, phytohormones involved in the symbiosis, SYM pathway signals, and R genes and specificity of rhizobia infection. This eBook will be a great reference book highlighting the research frontiers in legume-rhizobia symbiosis. |
| clc genomics workbench rna seq analysis: 2nd synthetic biology forum: system and synthetic biology for biofuels and bioproducts Jean Marie François, Min Jiang, Mingjie Jin, Shihui Yang, 2023-01-02 |
| clc genomics workbench rna seq analysis: The Burrows-Wheeler Transform: Donald Adjeroh, Timothy Bell, Amar Mukherjee, 2008-06-17 The Burrows-Wheeler Transform is one of the best lossless compression me- ods available. It is an intriguing — even puzzling — approach to squeezing redundancy out of data, it has an interesting history, and it has applications well beyond its original purpose as a compression method. It is a relatively late addition to the compression canon, and hence our motivation to write this book, looking at the method in detail, bringing together the threads that led to its discovery and development, and speculating on what future ideas might grow out of it. The book is aimed at a wide audience, ranging from those interested in learning a little more than the short descriptions of the BWT given in st- dard texts, through to those whose research is building on what we know about compression and pattern matching. The ?rst few chapters are a careful description suitable for readers with an elementary computer science ba- ground (and these chapters have been used in undergraduate courses), but later chapters collect a wide range of detailed developments, some of which are built on advanced concepts from a range of computer science topics (for example, some of the advanced material has been used in a graduate c- puter science course in string algorithms). Some of the later explanations require some mathematical sophistication, but most should be accessible to those with a broad background in computer science. |
| clc genomics workbench rna seq analysis: Organoids as Model Systems for Human Development, Disease and Clinical Applications Eumorphia Remboutsika, Thimios Mitsiadis, 2021-11-23 |
| clc genomics workbench rna seq analysis: Genotyping by Sequencing for Crop Improvement Humira Sonah, Vinod Goyal, S. M. Shivaraj, Rupesh K. Deshmukh, 2022-03-28 OGENOTYPING BY SEQUENCING FOR CROP IMPROVEMENT A thoroughly up-to-date exploration of genotyping-by-sequencing technologies and related methods in plant science In Genotyping by Sequencing for Crop Improvement, a team of distinguished researchers delivers an in-depth and current exploration of the latest advances in genotyping-by-sequencing (GBS) methods, the statistical approaches used to analyze GBS data, and its applications, including quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS) in crop improvement. This edited volume includes insightful contributions on a variety of relevant topics, like advanced molecular markers, high-throughput genotyping platforms, whole genome resequencing, QTL mapping with advanced mapping populations, analytical pipelines for GBS analysis, and more. The distinguished contributors explore traditional and advanced markers used in plant genotyping in extensive detail, and advanced genotyping platforms that cater to unique research purposes are discussed, as is the whole-genome resequencing (WGR) methodology. The included chapters also examine the applications of these technologies in several different crop categories, including cereals, pulses, oilseeds, and commercial crops. Genotyping by Sequencing for Crop Improvement also offers: A thorough introduction to molecular marker techniques and recent advancements in the technology Comprehensive explorations of the genotyping of seeds while preserving their viability, as well as advances in genomic selection Practical discussions of opportunities and challenges relating to high throughput genotyping in polyploid crops In-depth examinations of recent advances and applications of GBS, GWAS, and GS in cereals, pulses, oilseeds, millets, and commercial crops Perfect for practicing plant scientists with an interest in genotyping-by-sequencing technology, Genotyping by Sequencing for Crop Improvement will also earn a place in the libraries of researchers and students seeking a one-stop reference on the foundational aspects of – and recent advances in – genotyping-by-sequencing, genome-wide association studies, and genomic selection. |
| clc genomics workbench rna seq analysis: Advances in Bioinformatics Vijai Singh, Ajay Kumar, 2021-07-31 This book presents the latest developments in bioinformatics, highlighting the importance of bioinformatics in genomics, transcriptomics, metabolism and cheminformatics analysis, as well as in drug discovery and development. It covers tools, data mining and analysis, protein analysis, computational vaccine, and drug design. Covering cheminformatics, computational evolutionary biology and the role of next-generation sequencing and neural network analysis, it also discusses the use of bioinformatics tools in the development of precision medicine. This book offers a valuable source of information for not only beginners in bioinformatics, but also for students, researchers, scientists, clinicians, practitioners, policymakers, and stakeholders who are interested in harnessing the potential of bioinformatics in many areas. |
| clc genomics workbench rna seq analysis: Current Trends in Medicinal Plant Research and Neurodegenerative Disorders Muhammad Ayaz, Tahir Ali, Abdul Sadiq, Farhat Ullah, Muhammad Imran Naseer, 2022-07-28 |
| clc genomics workbench rna seq analysis: Inhibitory interneuron classification, function and dysfunction in neural network Thomas Claude Bienvenu, 2024-04-05 |
| clc genomics workbench rna seq analysis: Advancing the understanding of emergence of SARS-CoV-2 genetic variants and COVID-19 vaccine efficacy: Essential clinical and molecular insights and breakthroughs Alagarraju Muthukumar, Madhusudhanan Narasimhan, Ruben Luo, 2023-09-07 |
| clc genomics workbench rna seq analysis: Cancer Immunotherapy – Diagnostic and Therapeutic Strategies to Enhance Antitumoral Efficacies whilst Minimizing Toxicity Roza Nurieva, Sang T. Kim , Yeonseok Chung, 2024-10-21 With their unprecedented success, cancer immunotherapies including immune checkpoint inhibitors (ICIs), cancer vaccines, adoptive cell therapy (ATC), and immunomodulators are being increasingly used for various malignancies. Distinct from traditional treatments including surgery, radiation therapy, and chemotherapy, immunotherapeutics attempt to create long-lasting anti-tumor effects. However, only a minority of patients experience long-term benefits to single-agent immunotherapy, and most patients do not have initial responses to the immunotherapy or develop relapse after promising initial responses. Strategies to overcome immunotherapy resistance include (1) the development of biomarkers to select potential responders and/or exclude potential non-responders; and (2) the usage of combination treatments (ICIs, radiotherapy, chemotherapy, vaccines, fecal microbiota transplantation (FMT) and etc.) comprising different mechanisms of action and target multiple resistant mechanisms. At the same time, the possibility of new side effects due to the combinatorial strategies or the potential amplification of the well-known side effects of the ICIs, termed immune-related adverse events (irAEs), should be carefully monitored. |
| clc genomics workbench rna seq analysis: New Roles of Neutrophils and Granulocytic MDSC in Autoimmune Diseases, Inflammation, and Anti-microbial Immunity Dragana Odobasic, Marko Radic, Clare Hawkins, 2022-09-05 |
| clc genomics workbench rna seq analysis: Reverse Engineering of Regulatory Networks Sudip Mandal, 2023-11-07 This volume details the development of updated dry lab and wet lab based methods for the reconstruction of Gene regulatory networks (GRN). Chapters guide readers through culprit genes, in-silico drug discovery techniques, genome-wide ChIP-X data, high-Throughput Transcriptomic Data Exome Sequencing, Next-Generation Sequencing, Fuorescence Spectroscopy, data analysis in Bioinformatics, Computational Biology, and S-system based modeling of GRN. 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 protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Reverse Engineering of Regulatory Networks aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge. |
| clc genomics workbench rna seq analysis: Fat Metabolism and Deposition in Poultry: Physiology, Genetics, Nutrition and Interdisciplinary Research, Volume I Jie Wen, Sami Dridi, Elizabeth Ruth Gilbert, 2022-06-27 |
| clc genomics workbench rna seq analysis: Antimicrobial Resistance in Environmental Waters Karina Yew-Hoong Gin, Charmaine Ng, 2019-04-30 This Special Issue on Antimicrobial Resistance in Environmental Waters features 11 articles on the monitoring and surveillance of antimicrobial resistance (AMR) in natural aquatic systems (i.e., reservoirs, rivers), and effluent discharge from water treatment plants to assess the effectiveness of AMR removal and resulting loads in treated waters. Some of the key elements of AMR studies presented in this Special Issue highlight the underlying drivers of AMR contamination in the environment and the evaluation of the hazard imposed on aquatic organisms in receiving environments through ecological risk assessments. As described in this Issue, screening antimicrobial peptide (AMP) libraries for biofilm disruption and antimicrobial candidates are promising avenues for the development of new treatment options to eradicate resistance. |
| clc genomics workbench rna seq analysis: Early Life Stress-Induced Epigenetic Changes Involved in Mental Disorders Fushun Wang, Jason H. Huang, Fang Pan, Yi-Yuan Tang, 2021-08-09 |
| clc genomics workbench rna seq analysis: Regeneration from cells to limbs: Past, present, and future Jennifer R Morgan, Frank W Stahnisch, Pamela Imperadore, Fabio De Sio, 2023-07-03 |
| clc genomics workbench rna seq analysis: Insects at the Center of Interactions with Other Organisms Patrizia Falabella, Michel Cusson, Anne-Nathalie Volkoff, 2020-08-14 (A) Figure from Chami Kim-Jo, Jean-Luc Gatti and Marylène Poirié (2019). Drosophila Cellular Immunity Against Parasitoid Wasps: A Complex and Time-Dependent Process. Front. Physiol. 10:603. doi: 10.3389/fphys.2019.00603 (B) Figure from “Giuseppe Bari, Andrea Scala, Vita Garzone, Rosanna Salvia, Cem Yalcin, Pasqua Vernile, Antonella Maria Aresta, Osvaldo Facini, Rita Baraldi, Sabino A. Bufo, Heiko Vogel, Enrico de Lillo, Francesca Rapparini and Patrizia Falabella (2019). Chemical Ecology of Capnodis tenebrionis (L.) (Coleoptera: Buprestidae): Behavioral and Biochemical Strategies for Intraspecific and Host Interactions. Front. Physiol. 10:604. doi: 10.3389/fphys.2019.00604 (C) Figure from “Rosanna Salvia, Annalisa Grimaldi, Rossana Girardello, Carmen Scieuzo, Andrea Scala, Sabino A. Bufo, Heiko Vogel and Patrizia Falabella (2019). Aphidius ervi Teratocytes Release Enolase and Fatty Acid Binding Protein Through Exosomal Vesicles. Front. Physiol. 10:715. doi: 10.3389/fphys.2019.00715 (D) Figure from “Mariangela Coppola, Gianfranco Diretto, Maria Cristina Digilio, Sheridan Lois Woo, Giovanni Giuliano, Donata Molisso, Francesco Pennacchio, Matteo Lorito and Rosa Rao (2019). Transcriptome and Metabolome Reprogramming in Tomato Plants by Trichoderma harzianum strain T22 Primes and Enhances Defense Responses Against Aphids. Front. Physiol. 10:745. doi: 10.3389/fphys.2019.00745 (E) Figure from “Rosanna Salvia, Marisa Nardiello, Carmen Scieuzo, Andrea Scala, Sabino A. Bufo, Asha Rao, Heiko Vogel and Patrizia Falabella (2018). Novel Factors of Viral Origin Inhibit TOR Pathway Gene Expression X. Front. Physiol. 9:1678. doi: 10.3389/fphys.2018.01678 (F) Figure from “Sébastien Cambier, Olivia Ginis, Sébastien J. M. Moreau, Philippe Gayral, Jack Hearn, Graham N. Stone, David Giron, Elisabeth Huguet and Jean-Michel Drezen (2019). Gall Wasp Transcriptomes Unravel Potential Effectors Involved in Molecular Dialogues With Oak and Rose. Front. Physiol. 10:926. doi: 10.3389/fphys.2019.00926 (G) Figure from “Mariangela Coppola, Gianfranco Diretto, Maria Cristina Digilio, Sheridan Lois Woo, Giovanni Giuliano, Donata Molisso, Francesco Pennacchio, Matteo Lorito and Rosa Rao (2019). Transcriptome and Metabolome Reprogramming in Tomato Plants by Trichoderma harzianum strain T22 Primes and Enhances Defense Responses Against Aphids. Front. Physiol. 10:745. doi: 10.3389/fphys.2019.00745 (H) Figure from “Zbigniew Adamski, Sabino A. Bufo, Szymon Chowański, Patrizia Falabella, Jan Lubawy, Paweł Marciniak, Joanna Pacholska-Bogalska, Rosanna Salvia, Laura Scrano, Małgorzata Słocińska, Marta Spochacz, Monika Szymczak, Arkadiusz Urbański, Karolina Walkowiak-Nowicka and Grzegorz Rosiński (2019). Beetles as Model Organisms in Physiological, Biomedical and Environmental Studies – A Review. Front. Physiol. 10:319. doi: 10.3389/fphys.2019.00319 (I) Figure from “Surapathrudu Kanakala, Svetlana Kontsedalov, Galina Lebedev and Murad Ghanim (2019). Plant-Mediated Silencing of the Whitefly Bemisia tabaci Cyclophilin B and Heat Shock Protein 70 Impairs Insect Development and Virus Transmission. Front. Physiol. 10:557. doi: 10.3389/fphys.2019.00557 (J) Figure from “Rosanna Salvia, Annalisa Grimaldi, Rossana Girardello, Carmen Scieuzo, Andrea Scala, Sabino A. Bufo, Heiko Vogel and Patrizia Falabella (2019). Aphidius ervi Teratocytes Release Enolase and Fatty Acid Binding Protein Through Exosomal Vesicles. Front. Physiol. 10:715. doi: 10.3389/fphys.2019.00715 (K) Figure from “Lin Quan Ge, Sui Zheng, Hao Tian Gu, Yong Kai Zhou, Ze Zhou, Qi Sheng Song and David Stanley (2019). Jinggangmycin-Induced UDP-Glycosyltransferase 1-2-Like is a Positive Modulator of Fecundity and Population Growth in Nilaparvata lugens (Stål) (Hemiptera: Delphacidae). Front. Physiol. 10:747. doi: 10.3389/fphys.2019.00747 (L) Figure from “Zbigniew Adamski, Sabino A. Bufo, Szymon Chowański, Patrizia Falabella, Jan Lubawy, Paweł Marciniak, Joanna Pacholska-Bogalska, Rosanna Salvia, Laura Scrano, Małgorzata Słocińska, Marta Spochacz, Monika Szymczak, Arkadiusz Urbański, Karolina Walkowiak-Nowicka and Grzegorz Rosiński (2019). Beetles as Model Organisms in Physiological, Biomedical and Environmental Studies – A Review. Front. Physiol. 10:319. doi: 10.3389/fphys.2019.00319 (M) Figure from “Sébastien Cambier, Olivia Ginis, Sébastien J. M. Moreau, Philippe Gayral, Jack Hearn, Graham N. Stone, David Giron, Elisabeth Huguet and Jean-Michel Drezen (2019). Gall Wasp Transcriptomes Unravel Potential Effectors Involved in Molecular Dialogues With Oak and Rose. Front. Physiol. 10:926. doi: 10.3389/fphys.2019.00926 (N) Figure from “Gianandrea Salerno, Francesca Frati, Eric Conti, Ezio Peri, Stefano Colazza and Antonino Cusumano (2019). Mating Status of an Herbivorous Stink Bug Female Affects the Emission of Oviposition-Induced Plant Volatiles Exploited by an Egg Parasitoid. Front. Physiol. 10:398. doi: 10.3389/fphys.2019.00398 (O) Figure from “Marisa Skaljac, Heiko Vogel, Natalie Wielsch, Sanja Mihajlovic and Andreas Vilcinskas (2019). Transmission of a Protease-Secreting Bacterial Symbiont Among Pea Aphids via Host Plants. Front. Physiol. 10:438. doi: 10.3389/fphys.2019.00438 (P) Figure from “Alberto Santini and Andrea Battisti (2019). Complex Insect–Pathogen Interactions in Tree Pandemics. Front. Physiol. 10:550. doi: 10.3389/fphys.2019.00550 (Q) Figure from “Surapathrudu Kanakala, Svetlana Kontsedalov, Galina Lebedev and Murad Ghanim (2019). Plant-Mediated Silencing of the Whitefly Bemisia tabaci Cyclophilin B and Heat Shock Protein 70 Impairs Insect Development and Virus Transmission. Front. Physiol. 10:557. doi: 10.3389/fphys.2019.00557 (R) Figure from “Rosanna Salvia, Marisa Nardiello, Carmen Scieuzo, Andrea Scala, Sabino A. Bufo, Asha Rao, Heiko Vogel and Patrizia Falabella (2018). Novel Factors of Viral Origin Inhibit TOR Pathway Gene Expression X. Front. Physiol. 9:1678. doi: 10.3389/fphys.2018.01678 (S) Figure from “Sébastien Cambier, Olivia Ginis, Sébastien J. M. Moreau, Philippe Gayral, Jack Hearn, Graham N. Stone, David Giron, Elisabeth Huguet and Jean-Michel Drezen (2019). Gall Wasp Transcriptomes Unravel Potential Effectors Involved in Molecular Dialogues With Oak and Rose. Front. Physiol. 10:926. doi: 10.3389/fphys.2019.00926 (T) Figure from “Gong Chen, Qi Su, Xiaobin Shi, Huipeng Pan, Xiaoguo Jiao and Youjun Zhang (2018). Persistently Transmitted Viruses Restrict the Transmission of Other Viruses by Affecting Their Vectors. Front. Physiol. 9:1348. doi: 10.3389/fphys.2018.01348 (U) Figure from “Giuseppe Bari, Andrea Scala, Vita Garzone, Rosanna Salvia, Cem Yalcin, Pasqua Vernile, Antonella Maria Aresta, Osvaldo Facini, Rita Baraldi, Sabino A. Bufo, Heiko Vogel, Enrico de Lillo, Francesca Rapparini and Patrizia Falabella (2019). Chemical Ecology of Capnodis tenebrionis (L.) (Coleoptera: Buprestidae): Behavioral and Biochemical Strategies for Intraspecific and Host Interactions. Front. Physiol. 10:604. doi: 10.3389/fphys.2019.00604 (V) Figure from “Giuseppe Bari, Andrea Scala, Vita Garzone, Rosanna Salvia, Cem Yalcin, Pasqua Vernile, Antonella Maria Aresta, Osvaldo Facini, Rita Baraldi, Sabino A. Bufo, Heiko Vogel, Enrico de Lillo, Francesca Rapparini and Patrizia Falabella (2019). Chemical Ecology of Capnodis tenebrionis (L.) (Coleoptera: Buprestidae): Behavioral and Biochemical Strategies for Intraspecific and Host Interactions. Front. Physiol. 10:604. doi: 10.3389/fphys.2019.00604 (W) Figure from “Surapathrudu Kanakala, Svetlana Kontsedalov, Galina Lebedev and Murad Ghanim (2019). Plant-Mediated Silencing of the Whitefly Bemisia tabaci Cyclophilin B and Heat Shock Protein 70 Impairs Insect Development and Virus Transmission. Front. Physiol. 10:557. doi: 10.3389/fphys.2019.00557 (X) Figure from “Gianandrea Salerno, Francesca Frati, Eric Conti, Ezio Peri, Stefano Colazza and Antonino Cusumano (2019). Mating Status of an Herbivorous Stink Bug Female Affects the Emission of Oviposition-Induced Plant Volatiles Exploited by an Egg Parasitoid. Front. Physiol. 10:398. doi: 10.3389/fphys.2019.00398 |
| clc genomics workbench rna seq analysis: Efficient biomanufacturing via microbial cell factories, volume II Wei Luo, Zhenlin Han, Shuang Li, Yinjie Tang, 2023-09-29 |
| clc genomics workbench rna seq analysis: Celebrating 5 Years of Avian Physiology in Frontiers in Physiology Colin G. Scanes, Sandra G. Velleman, 2022-09-27 The avian physiology section is now five years old. This special e-book is to commemorate this event. For this highlights issue celebrating the first five years of the Avian Physiology section, it was decided to focus on the top papers/reviews published. Table 1 lists the top fifteen papers/reviews based on either views or down-loads as a pdf. There is some agreement between the two lists. What is compelling is that of the top papers, all except one encompasses research conducted in domesticated birds, predominantly with chickens with one focused on turkeys. It is perhaps not unexpected that research on chickens dominates the top papers because of the following: - Chickens are commercially important being the number one meat animal globally. - Chickens are used as the model species for birds. Other possibilities that could be the case include the following: - There are more researchers working on chickens compared to other commercial or wild species. - There are other avenues to publish wild bird research. - Lack of funding for open access article processing charges. The exceptions to the chicken papers/reviews is a paper on a passerine bird, the migratory blackheaded bunting (Emberiza melanocephala) (Singh et al., 2018) and a review paper focused on turkey satellite cell proliferation and differentiation (Velleman and Song, 2017). Of the top papers/reviews, six were related to muscle physiology (Bottje et al., 2017; Greene et al., 2019; Lassiter et al., 2019; Lin et al., 2017; Piekarski et al., 2020; Velleman and Song, 2017). These papers address different aspects of the physiology of muscle functioning and development in chickens or turkeys, specifically the following: - Small RNAs from the transcribed from mitochondrial genome in muscle (Bottje et al., 2017) - Leptin induced autophagy of muscle cells (Piekarski et al., 2020) - Proliferation and differentiation of myoblasts: influence of syndecan-4 and glypican-1 (Velleman and Song, 2017) - Myostatin signaling and muscle growth (Lassiter et al., 2019) The role of growth factors and signal transduction pathways in myoblast proliferation (Lin et al., 2017) - Muscle pathology, specifically, woody breast myopathy (Greene et al., 2019) There are also among the top papers/reviews on multiple diverse other organs and systems namely the following: adipose tissue (Abdalla et al., 2018), bone (Adhikari et al., 2019), feathering (Chen et al., 2019), gastro-intestinal functioning/microbiome (Li et al., 2018; Kraimi et al., 2018; Rodrigues et al., 2020), immune functioning (Bi et al., 2018; Wei et al., 2018), kidneys (Li et al., 2018), liver (Flees et al., 2017; Singh et al., 2018), endogenous opioids (Scanes and Pierzchala-Koziec, 2018), photoperiodism (Hanlon et al., 2020), pituitary gland (Zhang et al., 2021) and reproduction (Eusemann et al., 2018; Li et al., 2018). The geographical distribution of the top papers is interesting as summarized in Table 2. The United States of America and the People’s Republic of China were the country of origin of most of the papers. In addition, there were papers/reviews from Europe (France, Germany and a collaborative paper between researchers in the USA and Poland) and India. Of the top papers/reviews from the USA, six come from a single department, namely, the Department of Poultry Science/Center of Excellence for Poultry Science, University of Arkansas (Bottje et al., 2017; Flees et al., 2017; Green et al., 2019; Lassiter et al., 2019; Piekarski et al., 2020; Rodrigues |
| clc genomics workbench rna seq analysis: The Biogeochemistry, Biophysics, Radiobiology, and Technical Challenges of Deep Subsurface Research Geoffrey Battle Smith, Maria Antonella Tabocchini, Carlos Peña Garay, 2021-07-02 |
| clc genomics workbench rna seq analysis: Omics Technologies for Sustainable Agriculture and Global Food Security (Vol II) Anirudh Kumar, Rakesh Kumar, Pawan Shukla, Hitendra K. Patel, 2021-08-05 This edited book brings out a comprehensive collection of information on the modern omics-based research. The main focus of this book is to educate researchers about utility of omics-based technologies in rapid crop improvement. In last two decades, omics technologies have been utilized significantly in the area of plant sciences and has shown promising results. Omics technology has potential to address the challenge of food security in the near future. The comprehensive use of omics technology occurred in last two decades and helped greatly in the understanding of complex biological problems, improve crop productivity and ensure sustainable use of ecosystem services. This book is of interest to researchers and students of life sciences, biotechnology, plant biotechnology, agriculture, forestry, and environmental sciences. It is also a useful knowledge resource for national and international agricultural scientists. |
| clc genomics workbench rna seq analysis: Functional Genomics in Aquaculture Marco Saroglia, 2012-05-25 Genomics has revolutionized biological research over the course of the last two decades. Genome maps of key agricultural species have offered increased understanding of the structure, organization, and evolution of animal genomes. Building upon this foundation, researchers are now emphasizing research on genome function. Published with the World Aquaculture Society, Functional Genomics in Aquaculture looks at the advances in this field as they directly relate to key traits and species in aquaculture production. Functional Genomics in Aquaculture opens with two chapters that provide a useful general introduction to the field of functional genomics. The second section of the book focuses on key production traits such as growth, development, reproduction, nutrition, and physiological response to stress and diseases. The final five chapters focus on a variety of key aquaculture species. Examples looking at our understanding of the functional genomes of salmonids, Mediterranean sea bass, Atlantic cod, catfish, shrimp, and molluscs, are included in the book. Providing valuable insights and discoveries into the functional genomes of finfish and shellfish species, Functional Genomics in Aquaculture, will be an invaluable resource to researchers and professionals in aquaculture, genetics, and animal science. |
| clc genomics workbench rna seq analysis: Abiotic Stress Signaling in Plants: Functional Genomic Intervention Girdhar K. Pandey, Manoj Prasad, Amita Pandey, Maik Boehmer, 2016-08-08 Abiotic stresses such as high temperature, low-temperature, drought and salinity limit crop productivity worldwide. Understanding plant responses to these stresses is essential for rational engineering of crop plants. In Arabidopsis, the signal transduction pathways for abiotic stresses, light, several phytohormones and pathogenesis have been elucidated. A significant portion of plant genomes (Arabidopsis and rice were mostly studied) encodes for proteins involves in signaling such as receptor, sensors, kinases, phosphatases, transcription factors and transporters/channels. Despite decades of physiological and molecular effort, knowledge pertaining to how plants sense and transduce low and high temperature, low-water availability (drought), water-submergence, microgravity and salinity signals is still a major question for plant biologist. One major constraint hampering our understanding of these signal transduction processes in plants has been the lack or slow pace of application of molecular genomic and genetics knowledge in the form of gene function. In the post-genomic era, one of the major challenges is investigation and understanding of multiple genes and gene families regulating a particular physiological and developmental aspect of plant life cycle. One of the important physiological processes is regulation of stress response, which leads to adaptation or adjustment in response to adverse stimuli. With the holistic understanding of the signaling pathways involving not only one gene family but multiple genes or gene families, plant biologist can lay a foundation for designing and generating future crops, which can withstand the higher degree of environmental stresses (especially abiotic stresses, which are the major cause of crop loss throughout the world) without losing crop yield and productivity. Therefore, in this e-Book, we intend to incorporate the contribution from leading plant biologists to elucidate several aspects of stress signaling by functional genomics approaches. |
| clc genomics workbench rna seq analysis: Methane: A Bioresource for Fuel and Biomolecules Obulisamy Parthiba Karthikeyan, Deepak Kumaresan, Marina G. Kalyuzhanaya, Kirsten Heimann, Chettiyappan Visvanathan, Nidia S. Caetano, 2020-04-03 |
| clc genomics workbench rna seq analysis: Advancements in Forensic DNA Analysis Hirak Ranjan Dash, |
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Automation, Robotics and Mechatronics - Program Overview
Revolutionizing industries with cutting-edge automation. A career in automation and robotics involves working with cutting-edge technologies. Professionals in this field create intelligent …
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