ISCB News and Announcements

September 9, 2020 at 2:00PM EDT, Encyclopedia of DNA Elements (ENCODE) Phase III by Zhiping Weng, hosted by ISCB

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE and Roadmap Epigenomics data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

Hosted by:

• September 15, 2020 at 11:00 AM EDT, Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer by Luisa Escobar-Hoyos, hosted bv iRNA COSI and RNA Society
  
• NEW September 29, 2020 at 11:00AM EDT, Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic by Philippe Lemey, hosted by ISCB
  
• September 30, 2020 at 11:00AM EDT,  RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference by Alexey Kozlov, hosted by EvolCompGen COSI

Deadline: September 14, 2020

Special Sessions will consist of three broad categories:

• Focused workshops on specific research problems in computational biology and bioinformatics
• Software schools, aimed at providing training in new methods
• Activities focused on students and postdocs, or non-academic career opportunities

August 24, 2020 at 11:00AM EDT, Unravelling the Mystery of Orphan Genes to Understand the Origins of Genetic Novelty by Nikos Vakirlis
hosted by EvolCompGen and SMBE

What explains the presence of a gene only in the genome of one species and not in any other?  Species-specific protein-coding genes, also known as orphans, can arise "from scratch" from previously non-genic loci, through a process known as de novo gene emergence. How exactly the evolutionary transition from non-gene to functional gene unfolds is unclear. Can such denovo emerging genes increase an organism's fitness, and if so how? Orphan genes can also result from extensive sequence divergence of ancestral genes, which can eventually erase all similarity of a gene to its homologues in other species, a process even less well understood than de novo emergence.  I will present novel findings which advance our understanding of both these evolutionary mechanisms and bring us a small step closer to a complete picture of the origins of genetic novelty.

Hosted by:

Deadline:  September 14, 2020
Special Sessions will consist of three broad categories:

• Focused workshops on specific research problems in computational biology and bioinformatics
• Software schools, aimed at providing training in new methods
• Activities focused on students and postdocs, or non-academic career opportunities

The RECOMB/ISCB Conference on Regulatory and Systems Genomics (RSGDREAM 2020) invites abstracts for consideration for oral presentations or participation in a poster session. Abstracts may be either original unpublished work or original work that was published or accepted for publication in a high-impact journal between January 1, 2020 and November 1, 2020.

This conference is designed to present the latest findings about regulatory and systems genomics, foster discussion about current research directions, and establish new collaborations that will advance the development of a systems-level understanding of gene regulation. Some possible topics include:

• Network visualization and analysis
• Regulatory motifs and modules
• Epigenomics and chromatin state
• Non-coding RNAs
• Regulatory networks
• Co-transcriptional, post-transcriptional, and translational regulation
• Signal transduction networks
• Genetic, molecular, and phenotypic variation and human disease
• Cellular signatures of biological responses and disease states
• Mathematical modeling and simulation of biological systems
• Methods for systematic validation of high-throughput biological predictions
• Single-cell transcriptomics
• Single-cell proteomics
• Metabolomics
• Microbiome
• Machine learning methods for systems biology
• Translational systems biology

• Abstract Submission for Oral Presentation and Poster deadline: Monday, October 5, 2020
• Author notifications will occur on or around Monday, October 19, 2020
• Late Breaking Posters will have an open deadline until capacity is reached

Still time to submit!

Article Submissions
The Interface Focus Journal has committed to creating a special issue for this conference with up to twelve peer-reviewed articles.

Article submissions will close August 31st, initial review will be done and authors will have an opportunity to update and prepare their final manuscripts. The review period by the Royal Society will be from August 31st to September 30th. We will give authors two months to reply to comments in order to have the list of accepted articles at the end of September. Outstanding articles will be selected for featuring talks (10 total minutes in length with 2 minutes reserved for Q&A).

Authors are responsible for fees related to publishing as deemed by Royal Society.


Abstracts Submission for Flash Talks and Posters
ISCB-Latin America SoIBio BioNetMX Symposium on Bioinformatics 2020 invites abstracts topical to bioinformatics and computational biology for consideration for flash talk and/or poster presentation.

Abstracts will be selected for flash talk or poster presentation on the corresponding session. General Computation Biology abstracts will be accommodated in the closest area for the topic per recommendation of the reviewers. Conference areas:

• Bioinformatic strategies and methods to unravel RNA Genomics
• Computational Molecular Biology to Study Evolution in Microorganisms
• Development of Tools and Applications: Usability and Accessibility
• Ecology and Evolution
• Methods applied to Human Genetic studies
• Methods and Algorithms in Computational Molecular Biology
• Population dynamics and Evolution in Eukaryotes
• Strategies in Cancer Genomics: From family to population studies
• All other related areas
  
  

Mark your calendars for these upcoming ISCB Webinars!
Access to the webinar series is complimentary for all. Non ISCB Members must register

• August 11, 2020 at 11:00AM EDT, Protein Function Prediction using Graph Convolutional Networks with Language Model Features by Vladimir Gligorijevic, hosted by MLCSB
  
  
• August 24, 2020 at 11:00AM EDT, Unravelling the mystery of orphan genes to understand the origins of genetic novelty by Nikos Vakirlis, hosted by EvolCompGen and SMBE
  
  
• September 9, 2020 at 2:00 PM EDT, Encyclopedia of DNA Elements (ENCODE) Phase III by Zhiping Weng, hosted bv ISCB
  
  
• September 30, 2020 at 11:00AM EDT,  RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference by Alexey Kozlov, hosted by EvolCompGen COSI
  
  

GLBIO 2021 Special Session Deadline
Sept 14, 2020

If you are a member of ISCB, we encourage you to submit entries to the Science collection and Tutorial collection. Your submission entails a pointer to the science content, a short description of background or purpose (two lines) and lists your name as submitter. Submission will be subjected to a basic check of scope and purpose.

You find the relevant submission forms here - www.iscb.org/covid19-submissions.

• ISCB COVID-19 Statements. Here you find statements on the ongoing pandemic that have been issued by ISCB.
• ISCB COVID-19 Webinar collection. Here you find webinars specific to the topics of COVID-19 and Sars Cov-2 that are organized by ISCB.
• ISCB COVID-19 Science collection. Here you find materials specific to the topics of COVID-19 and Sars Cov-2 that have been submitted by ISCB members. This collection has three subsections for (i) scientific articles, (ii) scientific data sets and, (iii) proposals of community science projects.
• ISCB Tutorial collection. Here you find tutorials that present basic or advanced computational biology content for biologists and computational biologists in these times of increased digital education activity. The tutorials have been (i) presented at recent ISCB conferences and (ii) suggested by ISCB members.