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    Etc.: Steven Salzberg: 'What were they thinking?'
    Submitted by J.W. Bizzaro; posted on Wednesday, November 02, 2022

    Submitter

    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/

    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    We solicit submissions on previously unpublished research work.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
    Events: FREE! Register for VendorFest in Cambridge, Mass on October 27
    Submitted by Lisa Scimemi; posted on Thursday, October 13, 2022

    Submitter

    October 27, 2022
    Le Meridien Boston Cambridge
    Cambridge, Massachusetts, USA
    https://BiotechVendorFest.com

    Join us for VendorFest Cambridge, a highly targeted trade show that will feature leading vendors serving the biopharma industry. This year's event will be taking place October 27 from 12-4pm at the Le Meridien Boston Cambridge.

    Why Attend VendorFest Cambridge?
    • Discover the latest products & services from life science suppliers
    • Local area event - close to Kendall and Central Square
    • VendorFest is 4 hours long, come when it is convenient for you during the day (12pm-4pm)
    • Network with industry peers, after 2 years of no face-to-face events
    • Enjoy a Oktoberfest themed event with food and German beer and wine tastings
    • Participate in hourly exhibit hall raffles
    • Have a new social media headshot taken by a professional photographer
    • Attend VendorFest Cambridge at no cost!
    Just some of the exhibitors include:
    Abcam, Akadeum Life Sciences, Inc., Asymchem, Berkshire Sterile Manufacturing, Biocytogen, BioDuro-Sundia, Biomedical Search Consultants, Bio-Techne, Boston University Questrom School of Business, Cell Microsystems, Clinlab Staffing, Conductive Technologies, eLabNext, Erbi Biosystems Inc., Hamilton Storage, JoVE, KCAS Bioanalytical & Biomarker Services, Kibur Medical, LevitasBio, MERIT CRO, Medchemexpress LLC, Mettler Toledo Rainin, NFP, PerkinElmer, Reaction Biology, RedShiftBio, Sanguine Bio, Sartorius, Scientist.com, Siemens Healthineers, STAT, Suffolk University, Unchained Labs, WuXi Biologics, Zaether, Ziath and more.

    For more information and to register for your FREE pass to VendorFest Cambridge, visit: https://BiotechVendorFest.com.
    Awards: 2022 Nobel Prize in Physiology or Medicine
    Submitted by J.W. Bizzaro; posted on Tuesday, October 04, 2022

    Submitter

    The Nobel Assembly at Karolinska Institutet decided yesterday to award the 2022 Nobel Prize in Physiology or Medicine to Svante Pääbo for his discoveries concerning the genomes of extinct hominins and human evolution.

    EXCERPT

    Humanity has always been intrigued by its origins. Where do we come from, and how are we related to those who came before us? What makes us, Homo sapiens, different from other hominins?

    Through his pioneering research, Svante Pääbo accomplished something seemingly impossible: sequencing the genome of the Neanderthal, an extinct relative of present-day humans. He also made the sensational discovery of a previously unknown hominin, Denisova. Importantly, Pääbo also found that gene transfer had occurred from these now extinct hominins to Homo sapiens following the migration out of Africa around 70,000 years ago. This ancient flow of genes to present-day humans has physiological relevance today, for example affecting how our immune system reacts to infections.

    Pääbo's seminal research gave rise to an entirely new scientific discipline; paleogenomics. By revealing genetic differences that distinguish all living humans from extinct hominins, his discoveries provide the basis for exploring what makes us uniquely human.
    Press release: https://www.nobelprize.org/prizes/medicine/2022/press-release/

    Submitter

    Would you like to see an interactive virus capsid model quickly and easily? Slab it or cut it in half? A clathrin coat? A bacterial gas vesicle? The mysterious "vault" eukaryotic nanocompartment?

    https://proteopedia.org/w/FirstGlance/Virus_Capsids_and_Other_Large_Assemblies

    The views at the above link were obtained with Version 4.0 of FirstGlance in Jmol released August 15, 2022 (free and open source; google "firstglance" as one word, or http://firstglance.jmol.org). Newly, it automatically constructs "biological assemblies" and shows "biomolecule 1" in its initial view. Exploring the asymmetric unit is then an option.

    Very large assemblies+++ are automatically simplified to alpha carbons, or a subset of alpha carbons; see examples at the above link. What are such simplified models good for? They can be measured, colored by secondary structure, hydrophobic/polar, charge, amino-to-carboxy rainbow, or evolutionary conservation (if pre-processed by the ConSurf Server). Each group of sequence-identical chains can be assigned a distinct color (under Solid in the Views tab).

    You can make an animation, ready to drop into a presentation slide, from any view in FirstGlance. It takes just a few mouse clicks. Examples in Google Slides:

    http://tinyurl.com/movingmolecules

    A small assembly, 2acz, has 4 chains in its asymmetric unit, and 12 chains in its biomolecule 1. You will be offered the option to simplify, so you can try it both ways. Even simplified to alpha carbons, the transmembrane helices stand out with the hydrophobic/polar and charge views. Its construction can be understood by giving a distinct color to each of the 4 sequence-distinct protein chains (Solid in the Views tab).

    http://firstglance.jmol.org/fg.htm?mol=2acz

    Structural biologists: With FirstGlance, you can't miss (after clicking "Show more details") incomplete sidechains, missing residues, alternate locations (can be animated), occupancy < 1.0 (all exemplified in 1ijw). All salt bridges can be displayed with one click (Tools tab), and a spreadsheet-ready list is reported with one more click. A "Contacts & Non-Covalent Interactions" tool makes it easy to visualize the interactions with any moiety you specify. Protein crosslinks are automatically detected and highlighted/zoomed with a few clicks: isopeptides, thioesters, thioethers, his-tyr, lys-cys NOS as well as, of course, disulfides. Step by step:

    https://proteopedia.org/w/FirstGlance/Evaluating_Protein_Crosslinks

    Electron density maps (or EM density maps) can be displayed for anything selected with the Find.. dialog, as well as crosslinks and ends of chains. See examples from FirstGlance here:

    https://proteopedia.org/w/Electron_density_maps

    New color schemes for simplified models:

    http://firstglance.jmol.org/notes.htm#bucolors

    New color schemes for simplified models:

    http://firstglance.jmol.org/notes.htm#bucolors

    To clear the old version of FirstGlance out of your browser's cache, go to

    http://firstglance.jmol.org/fg.htm?mol=1ijw

    Then regardless of whether the molecule displays, hold down the Shift key while you Reload.

    +++"Very large assemblies" means >25,000 non-hydrogen atoms. Only about 3% of entries in the World-Wide Protein Data Bank have biological assemblies that large. However, these include very important structures, such as virus capsids. Simplification rules:

    http://firstglance.jmol.org/notes.htm#simplification
    Events: EDGE: A global undergraduate STEM conference
    Submitted by Frank Lee; posted on Friday, August 12, 2022

    15 November 2022
    Location: Hybrid
    https://www.edge-stem.org

    EDGE is a global non-profit undergraduate conference, which welcomes submissions of student research from all areas of STEM. The overarching aim of this conference is to give students a platform where they are able to showcase their original research in different STEM fields, encourage dialogue, and thereby promote the practice of STEM research more generally. Furthermore, by inviting established researchers in different fields as keynote speakers, we look to provide an opportunity for students to learn about the value and inner workings of academia, and grow their academic network.

    REGISTRATION

    Registration is free and special awards await the best paper, best presentation, and best researcher at the conference.

    TOPICS OF INTEREST

    Any papers related in STEM areas are welcome. We are especially looking forward to papers related to the following areas:
    • Applied sciences
    • Biological sciences
    • Computer science
    • Health sciences
    • Physical sciences
    • Neuroscience
    • Mathematics

    IMPORTANT DATES

    Deadline for abstract submission: 31 August 2022
    Deadline for paper submission: 20 September 2022
    Notification of acceptance: 20 October 2022
    Conference date: 15 November 2022

    GUIDE FOR AUTHORS

    • Please limit your abstract to 300 words.
    • The paper must adhere to any of the standard citation formats. It must have a word limit of 5000 words. The format for the file name is LASTNAME.FIRSTNAME.SUBJECT-AREA.TITLE (e.g. Smith.Bob.Biology.The Evolution of Tool Use in Primates).
    • Submit your abstract and paper to submission[at]edge-stem.org.
    • Each participant is given 15 minutes to present their paper. There will be a 5-minute Q&A portion after the presentation. Everyone is encouraged to use a slide deck which must be sent to the organizing committee prior to the conference.

    FOR MORE INFORMATION

    For all general inquiries, please contact: submission[at]edge-stem.org.

    Submitter

    August 7-9, 2022
    Philadelphia, PA, USA
    https://icibm2022.iaibm.org

    Dear Colleagues:

    The 10th International Conference on Intelligent Biology and Medicine (ICIBM 2022) will take place Philadelphia, PA, USA August 7-9, 2022, https://icibm2022.iaibm.org. ICIBM is a high caliber conference which brings together eminent scholars with expertise in various fields of computational biology, systems biology, computational medicine, as well as experimentalists interested in 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.

    Our keynote include Drs. Xihong Lin, Ludmil Alexandrov, Smita Krishnaswamy, Mona Singh. Eminent Scholars includes:Drs. Feixiong Cheng, Jiang Qian, Yuan Luo, Li Shen, Derrick Scott, Lana Garmire.

    Registration is open. Please join us.

    ICIBM 2022 Organization Committee

    The web service Hiplot has been published in the journal Briefings in Bioinformatics.

    ABSTRACT

    Complex biomedical data generated during clinical, omics and mechanism-based experiments have increasingly been exploited through cloud-and visualization-based data mining techniques. However, the scientific community still lacks an easy-to-use web service for the comprehensive visualization of biomedical data, particularly high-quality and publication-ready graphics that allow easy scaling and updatability according to user demands. Therefore, we propose a community-driven modern web service, Hiplot (https://hiplot.org), with concise and top-quality data visualization applications for the life sciences and biomedical fields. This web service permits users to conveniently and interactively complete a few specialized visualization tasks that previously could only be conducted by senior bioinformatics or biostatistics researchers. It covers most of the daily demands of biomedical researchers with its equipped 240+ biomedical data visualization functions, involving basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modelling, etc. Moreover, to improve the efficiency in use and development of plugins, we introduced some core advantages on the client-/server-side of the website, such as spreadsheet-based data importing, cross-platform command-line controller (Hctl), multiuser plumber workers, JavaScript Object Notation-based plugin system, easy data/parameters, results and errors reproduction and real-time updates mode. Meanwhile, using demo/real data sets and benchmark tests, we explored statistical parameters, cancer genomic landscapes, disease risk factors and the performance of website based on selected native plugins. The statistics of visits and user numbers could further reflect the potential impact of this web service on relevant fields. Thus, researchers devoted to life and data sciences would benefit from this emerging and free web service.

    CITATION

    Jianfeng Li et al. "Hiplot: a comprehensive and easy-to-use web service for boosting the publication-ready biomedical data visualization." Briefings in Bioinformatics, bbac261 (2022). https://doi.org/10.1093/bib/bbac261.

    AVAILABILITY

    Website: https://hiplot.org

    Submitter

    We are happy to announce a new web server and standalone software, HLAncPred, developed for predicting non-classical HLA binders.

    Web server link: https://webs.iiitd.edu.in/raghava/hlancpred/

    Paper link: https://doi.org/10.1093/bib/bbac192

    Submitter

    December 6-9, 2022
    International Conference on Bioinformatics and Biomedicine (BIBM 2022)
    Las Vegas, NV, USA
    https://ieeebibm.org/BIBM2022/

    Network Science and Artificial Intelligence for Biomedicine & Health informatics (NSAIBHI) Workshop:
    Network Science is a new paradigm of study to understand complex systems including biological interactions. Pharmacology and drug discovery leverage network biology advances for a better understanding of the complex interactions between drugs, targets and disease, for designing new molecule, and for identifying drugs to be successfully repurposed. More recently, graph neural networks expressed to be a potential game changer in deciphering the inherent complex interaction patterns in complex networks.

    The workshop and the foreseen special issue intend to highlight novel research in the area of network science, network biology and network medicine coupled with representation learning and its application to biology, medicine, and pharmacology. The focus is on, but not limited to, the following broad areas:

    1. Network Representation Learning
    2. Graph Convolution Neural Network
    3. Network Embedding
    4. Heterogeneous network integration
    5. Network Alignment
    6. Disease module detection
    7. Network Drug Discovery and Repurposing

    IMPORTANT DATES

    Electronic submission of full papers: Aug, 21, 2022
    Notification of paper acceptance: Oct 21, 2022
    Main conference Camera-ready of accepted papers: Nov 12, 2022
    Workshop Paper Camera-ready of accepted papers: Nov 12, 2022
    Conference: Dec. 6-9, 2022

    PROCEEDINGS

    All workshop accepted papers and posters will appear in the IEEE Conference Proceedings.

    A special issue on a Scopus Indexed Journal is planned, negotiations are in progress, journals will be communicated in an upcoming announcement.
    Submit Archive Subscribe

     

    Acknowledgments

    We wish to thank the following for their support:

    [University of Birmingham]
    [Regeneron]
    [Become a sponsor]
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