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We're pleased to inform you that we're working on an edited collection with the working title, Next Generation Sequencing: Standard Operating Procedures and Applications. Jeff Bizzaro and I are the editors, and we anticipate that the collection will comprise protocols, standard operating procedures and best practices in NGS data analysis.
The book will be published by CRC Press / Taylor and Francis.
CALL FOR CHAPTERS
We are looking for contributed chapters on the following topics or subtopics, including specific tools:
Quality Control:
Read Alignment:
Variant Calling:
Transcriptome Assembly:
Differential Expression Analysis:
Functional Annotation:
- DAVID
- Gene Ontology (GO) enrichment
- KEGG pathway analysis
Clustering and Classification:
- Principal component analysis (PCA)
- Hierarchical clustering
- Machine learning algorithms
Epigenetics:
- ChIP-seq
- ATAC-seq
- RNA-seq
Metagenomics:
- QIIME
- MOTHUR
- MG-RAST
- MetaPhlAn
EDITORS
Prashanth N. Suravajhala, Ph.D. is a Principal Scientist at Amrita School of Biotechnology, India. With over 7 years of postdoctoral experience, he led projects in systems genomics and next-gen sequencing analysis. He explores unknown regions of the human genome, focusing on top-down systems biology of hypothetical proteins and has developed an interest in long noncoding RNAs. Prashanth has over 90 peer-reviewed publications, edited 3 books, and advocates for open access and open science. He founded Bioclues.org, India's largest bioinformatics society. He can be reached at https://www.bioinformatics.org/wiki/Prash
J.W. Bizzaro, M.Sc. is co-founder of Bioinformatics.org, a professional network that provides various resources to professionals in the field of bioinformatics while advancing open source software and open access research. He has been involved in the field for more than 25 years and has made significant contributions to the development of bioinformatics software, including MeltSim, a DNA melting simulator. His research interests include structural and evolutionary genomics. He can be reached at https://www.bioinformatics.org/wiki/J.W._Bizzaro
CONTACT
If you would like to contribute or would like more information, please contact: prash[at]bioclues.org
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May 16-18, 2023
Boston, MA
https://www.bio-itworldexpo.com/bioinformatics
Leverage Computational Tools and Methods to Turn Big Data into Smart Data to Advance Pharma R&D.
The Bioinformatics track taking place May 16-18, 2023 at the 22nd Annual Bio-IT World Conference & Expo in Boston, MA assembles thought leaders who will present case studies using computational resources and tools that take multimodal data analyses across genomics, transcriptomics, proteomics, metabolomics, and other data types (e.g., imaging), and align it with clinical action. Turning big data into smart data can lead to real-time assistance in disease prevention, prognosis, diagnostics, and therapeutics. With the ever-increasing volume of information generated for curing or treating diseases and cancers, bioinformatics technologies, tools, and techniques play a critical role in turning data into actionable knowledge to meet unstated and unmet medical needs. Other themes we will explore include new methods of single-cell data analysis, how bioinformatics can leverage tools/methods from data science and AI to advance research, and deep learning approaches to help with applications of bioinformatics to pharma R&D.
Speakers – and potential collaborators – from Tonix Pharmaceuticals Holding Corporation; Tempus; Baylor College of Medicine; Golden Helix, Inc.; Weill Cornell Medicine; Seven Bridges; Seqera Labs; Biomage; Snowflake; Zifo; Qiagen; The University of Texas MD Anderson Cancer Center; Harbor UCLS Medical Center; University of Illinois at Chicago; Mohammed Bin Rashid University of Medicine & Health Sciences (MBRU); BioTeam; NIH NIAID; Makerere University, Kampala, Uganda; Code Ocean; Massachusetts General Hospital; ENDEPUS Research, Inc./University Aix Marseille; University of North Dakota, and elsewhere offer insights into areas such as:
- Bioinformatics for Precision Medicine
- Non-Coding RNA and Ribotherapeutics for Post-Genomic Precision Medicine
- R&D Workflows to Accelerate Science
- Bioinformatics and Data-Intensive Sciences: Building Technology and Infrastructure Foundations for Global Growth
- Statistical Methods and Techniques to Develop Meaningful Insights from Datasets
By attending this program, you will:
- Explore key strategies and implementation examples of NGS labs to be successful long term.
- Hear about remapping approaches of the GRCh38 reference genome to gain improved insights from existing data.
- Explore the intersection of multi-omic and clinic-pathological disease stratification to personalize drug R&D.
- Learn about strategies for containing cloud computing costs in healthcare and life sciences.
- Discuss insights from running the most widely used cloud-based system for single cell RNA-seq data analysis.
- Learn about cutting-edge computation with genome-scale experimentation to highlight the inexorable progress of sequence-based precision medicine in targeting non-coding RNA causes of human disease with RNA-based drugs.
- Hear about global collaborative efforts in working with the African Centers of Excellence (ACE) in bioinformatics and data-intensive sciences to build the technology and infrastructure foundations for sustainable, energy systems.
- Explore how to best manage the creative chaos of the computational research data lifecycle.
- Understand data analytics on economic information that impacts medical decision-making processes.
- Network and meet with 2,500+ senior level informatics experts and IT professionals from pharma, biotechnology and academia from over 30+ countries who are attending the Bio-IT World Conference & Expo
- Educate yourself with the latest technologies and services in our exhibit hall
Hear the above and more first-hand experiences and case studies in the Bioinformatics track, taking place May 16-18, 2023 in Boston, MA.
We are planning for this track to be presented in-person in Boston, Mass, as well as offering online platform in parallel for those who want to participate virtually from anywhere in the world. For more details on the program agenda and speaker line-up, please visit https://www.bio-itworldexpo.com/bioinformatics
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May 8-12, 2023
https://www.transmittingscience.com/courses/statistics-and-bioinformatics/introduction-bayesian-inference-practice/
Registration is open for the course Introduction to Bayesian Inference in Practice – 6th edition. This course will be held live online (synchronous). Max 18 participants.
Dates: May 8th-12th, 2023. Online live sessions from Monday to Friday; 13:00 to 17:00 (Madrid time zone).
Instructors: Dr. Daniele Silvestro (University of Gothenburg, Sweden) and Tobias Andermann (University of Gothenburg, Sweden)
COURSE OVERVIEW
This course is based on the assumption that the easiest way to understand the principles of Bayesian inference and the functioning of the main algorithms is to implement these methods yourself.
The instructor will outline the relevant concepts and basic theory, but the focus of the course will be to learn how to do Bayesian inference in practice. He will show how to implement the most common algorithms to estimate parameters based on posterior probabilities, such as Markov Chain Monte Carlo samplers, and how to build hierarchical models.
He will also touch upon hypothesis testing using Bayes factors and Bayesian variable selection.
The course will take a learn-by-doing approach, in which participants will implement their own MCMCs using R or Python (templates for both languages will be provided).
After completion of the course, the participants will have gained a better understanding of how the main Bayesian methods implemented in many programs used in biological research work. Participants will also learn how to model at least basic problems using Bayesian statistics and how to implement the necessary algorithms to solve them.
Participants are expected to have some knowledge of R or Python (each can choose their preferred language), but they will be guided "line-by-line" in writing their script. The aim is that, by the end of the week, each participant will have written their own MCMC – from scratch! Participants are encouraged to bring own datasets and questions and we will (try to) figure them out during the course and implement scripts to analyze them in a Bayesian framework.
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September 6-7, 2023
Padua, Italy
https://cibb2023.dei.unipd.it/call-for-special.html
Distributed computing systems have become pivotal in the analysis of bioinformatics data, especially for the investigation of complex biological problems that require intense computational workloads. The usage of distributed computing systems like Apache Spark, in fact, might allow scientific discoveries on bioinformatics data that otherwise would be impossible if the analyses were performed on personal computers.
Our special session on "Distributed computing in bioinformatics and computational biology" aims at calling for researchers able to show the potential and the advance of distributed computing resources to make accurate computational analyses in biological datasets.
With this special session, we would like to gather scientific contributions aimed at optimizing the usage of distributed computing systems and resources in any bioinformatics, genomics, and proteomics context. The results presented in these studies would be useful and helpful both for the distributed computing experts and for inexperienced users approaching this subject for the first time.
Topics of interest include:
- Distributed computing systems in genomics and proteomics
- Bioinformatics projects enhanced by distributed computing platforms
- Optimization of distributed computing systems
- Application of machine learning methods to bioinformatics datasets enhanced through distributed computing
- Protocols for efficient usage of distributed computing systems
Special session organizers:
Davide Chicco , University of Toronto, Canada
Umberto Ferraro Petrillo , Sapienza Università di Roma, Italy
Giuseppe Cattaneo , Università di Salerno, Italy
Raffaele Giancarlo , Università di Palermo, Italy
Lorenzo Di Rocco , Sapienza Università di Roma, Italy
Giorgio Grani , Sapienza Università di Roma, Italy
IMPORTANT DATES
Short paper submission: April 30, 2023
Acceptance/rejection notification: June 9, 2023
Camera-ready short paper submission: June 23, 2023
Conference: September 6-8, 2023
PROCEEDINGS
The proceedings will not be indexed on Scopus, but, after the conference, the authors of all the accepted short papers presented at the conference will be invited to submit an extended version of their manuscripts to the conference proceedings book in Springer Lecture Notes in Bioinformatics (LNBI), or to a supplement in a journal such as BMC Bioinformatics or BMC Medical Informatics and Decision Making.
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July 16-19, 2023
Tampa, FL, USA
https://icibm2023.iaibm.org
Dear colleagues,
We are pleased to announce the 11th International Conference on Intelligent Biology and Medicine (ICIBM 2023), which will take place in Tampa, FL, USA. ICIBM is a high-caliber conference that brings together eminent scholars with expertise in various fields of computational biology, systems biology, computational medicine, and experimentalists interested in the application of computational methods in biomedical studies. The purpose of the ICIBM is to provide a congenial atmosphere highly conducive to extensive discussion and networking. You are invited to submit papers and abstracts with unpublished, original work describing recent advances in all aspects of Bioinformatics, Intelligent Computing, Systems Biology, and Medical Informatics, including but not restricted to the following topics:
Bioinformatics:
- Genomics and genetics/epigenetics, including integrative & functional genomics, genome evolution, GWAS.
- Next-generation sequencing data analysis, 3D genome.
- Big data science including storage, analysis, modeling, visualization, and cloud.
- Precision medicine, translational bioinformatics, and medical informatics.
- Drug discovery, design, and re-purposing.
- Proteomics, and protein structure prediction, function and interactions.
- Single-cell sequencing data analysis.
- Microbiome and Metagenomics.
Intelligent Computing and Data Science:
- Artificial intelligence, machine learning, deep learning, data mining, knowledge discovery.
- Natural language processing, literature mining, semantic ontology, and health informatics.
- Neural computing, kernel methods, feature selection/extraction.
- Evolutionary computing, swarm intelligence / optimization, ensemble methods.
- Artificial life and artificial immune system.
- Biomedical image analysis and processing.
Systems Biology:
- Modeling and simulation of biological processes, pathways, networks, and interactomes.
- Modeling of cellular and multi-cellular interaction systems.
- Multi-dimensional omics data integration.
- Synthetic biological systems.
- Metabolomics, microbiome, and lipidomics.
- Self-organization in living systems (cells, organisms, swarms, ecosystems, etc.).
Medical Informatics:
- Cohort discovery, EHR-based phenotyping, Predictive Modeling.
- Data quality assessment or validation.
- Clinical decision support solutions.
- Informatics to address disparities in health and health care.
- Interoperability (e.g., ontology, terminology, standards, and others).
- Machine learning for clinical applications, genome and phenome analysis/associations.
- Mobile health and wearable devices.
- Human-computer interaction and human factors.
PAPER SUBMISSION AND PUBLICATION
Prospective authors are invited to submit unpublished work to ICIBM 2023. All papers and abstracts will be initially submitted through the EasyChair conference system (link on the website). Selected papers of the registered authors will be recommended to be published in special issues in the following journals, subject to additional editorial approval and expected additional review by each journal: Cancers (IF: 6.24), Genes (IF: 4.37), Chemistry & Biodiversity (IF: 2.74, no publication fee), Quantitative Biology (no publication fee), and Informatics (IF coming soon).
ABSTRACT SUBMISSION
Conference participants are invited to submit abstracts to ICIBM 2023. The abstract submitted to the conference should be formatted using the abstract template provided on the conference website. The abstract body should be no more than 400 words. We welcome submissions of highlight papers that have been recently published or accepted for publication. In this case, the abstract should include a complete reference to the published paper. A group of experts will evaluate the submissions and select the abstracts to be presented orally or as a poster. Please submit your abstract through the EasyChair Conference System (link on the website).
TRAVEL AWARDS
The goal of the ICIBM 2023 Travel Award is to encourage the participation of young scientists in training, including graduate, undergraduate, and high school students, as well as postdoctoral fellows. Specific consideration will be given to qualified applicants from underrepresented populations, minority institutes, female trainees, or those who need special financial support to attend ICIBM 2023.
IMPORTANT DATES
Deadline for original paper submission: March 01 (Wednesday), 2023
Notification to authors of papers: May 12 (Friday), 2023
Deadline for abstract submission: May 30, 2023
Conference early registration opens: June 1, 2023
Conference early registration deadline: June 20 (Tuesday), 2023
Deadline for travel award application: June 16 (Friday), 2023
Conference regular registration: June 21 – July 16, 2023
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EXCERPT
A new artificial intelligence (AI) system called AlphaCode is bringing humanity one step closer to that vision, according to a new study. Researchers say the system – from the research lab DeepMind, a subsidiary of Alphabet (Google's parent company) – might one day assist experienced coders, but probably cannot replace them.
"It's very impressive, the performance they're able to achieve on some pretty challenging problems," says Armando Solar-Lezama, head of the computer assisted programming group at the Massachusetts Institute of Technology.
Source: https://www.science.org/content/article/ai-learns-write-computer-code-stunning-advance
DeepMind: https://www.deepmind.com
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It is with much sadness that we inform you all that Simon Gladman passed away last week. A Galaxy community leader, he was an architect of the Galaxy app and Australia Biocommons.
More information: https://www.biocommons.org.au/news/simon-gladman
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Johns Hopkins computational biologist and 2013 Franklin Award laureate Steven Salzberg says controversial Boston University study that created a potentially deadly form of the omicron coronavirus variant should never have happened.
EXCERPT
The BU study took part of one virus, omicron, and part of another virus – what they were calling the Washington State virus, but think of it as the original strain that came to the U.S. from Wuhan, China, in early 2020. They took a very small part of the genome of omicron virus – the spike protein, which lets the virus break into the host cells – and combined it with the rest of the genome from the Washington State virus, which they called the backbone. And they said, "Let's see what happens!" And that's where people like me say, "What the heck are you thinking?"
Full story: https://hub.jhu.edu/2022/11/01/steven-salzberg-advises-ending-gain-of-function-research/
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June 22-24, 2023
L'Aquila, Italy
https://2023.cbms-conference.org
CALL FOR PAPERS
Attracting a worldwide audience, CBMS is the premier conference for computer-based medical systems, and one of the main conferences within the fields of medical informatics and biomedical informatics. CBMS allows the exchange of ideas and technologies between academic and industrial scientists. The scientific program of IEEE CBMS 2023 will consist of regular and special track sessions with technical contributions reviewed and selected by an international program committee as well as keynote talks, and tutorials given by leading experts in their fields. The IEEE CBMS 2023 edition also aims to host high-quality papers about industry and real case applications as well as allow to researchers leading international projects to show to the scientific community the main aims, goals, and results of their projects.
We solicit submissions on previously unpublished research work. Example areas include but are not limited to:
- Biomedical Signal and Image Processing
- Clinical and Healthcare Services Research
- Data Analysis and Visualization
- Data Mining and Machine Learning
- Decision Support and Recommendation Systems
- Healthcare Communication Networks
- Healthcare Data and Knowledge Management
- Human-Computer Interaction (HCI) in Healthcare
- Information Technologies in Healthcare
- Digital Biomarkers
- Intelligent Medical Devices and Smart Technologies
- Radiomics and Radiogenomics
- Semantics and Knowledge Representation
- Serious Gaming in Healthcare
- Systems Integration and Security
- Technology-enabled Education
- Telemedicine Systems
- Translational Bioinformatics
- Sensor solutions for Connected Health
- mHealth Solutions and Insights
- Learning from Medical Devices
- Cyberphysical Systems in Medicine
ORGANIZERS
Prof. Giuseppe Placidi, PhD, Università dell'Aquila (Italy)
Rosa Sicilia, PhD, Università Campus Bio-Medico di Roma (Italy)
Prof. Alejandro Rodríguez González, PhD, Universidad Politécnica de Madrid (Spain)
PAPER SUBMISSION AND PUBLICATION
- Submitted papers have to be original, containing new and original results.
- Submission implies the willingness of at least one of the authors to register and present the paper at the CBMS 2023 Symposium.
- All papers will be peer reviewed by at least two independent referees.
- Prospective authors are invited to submit papers in any of the topics listed above.
- Instructions for preparing the manuscript (in Word and Latex formats) are available at: https://2023.cbms-conference.org/general-instructions/
- Please also check the Guidelines.
- Papers must be submitted electronically via the web-based submission system.
IMPORTANT DATES
Deadline for special track proposal: November 10, 2022
Special track notification acceptance: November 20, 2022
Paper submission deadline: February 15, 2023
Notification of acceptance: March 30, 2023
Camera-ready due: April 18, 2023
CONTACTS
cbms2023[at]cbms-conference.org
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| Acknowledgments |
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We wish to thank the following for their support:
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