Call for Papers
IEEE BIBM 2020 Workshop on Long Non-Coding RNAs: Mechanism, Function, and Computational Analysis (BIBM-LncRNA)
Welcome to the workshop on Long Non-Coding RNAs: Mechanism, Function, and Computational Analysis (BIBM-LncRNA 2020) to be held in December 2020, in conjunction with IEEE BIBM 2020 conference holding vurtually / online.
The recent application of high throughput technologies to transcriptomics has changed our view of gene regulation and function. The discovery of extensive transcription of large RNA transcripts, termed long noncoding RNAs (lncRNAs), provide an important and new perspective on the centrality of RNA in gene regulation. LncRNAs are involved in various biological and cellular processes, such as genetic imprinting, chromatin remodeling, gene regulation and embryonic development. LncRNAs have been implicated in several chronic diseases, such as cancers, and heart disease, etc. Given the abundance of lncRNAs, tens of thousands still need to be functionally characterized. Various types of genomic data on lncRNAs are currently available, including sequences, secondary/tertiary structures, transcriptome data, and their interactions with related proteins or genes. The key challenge is how to integrate data from myriad sources to determine the functions and the regulatory mechanism of these ubiquitous lncRNAs. Computational studies of lncRNA secondary, tertiary structure, and lncRNA interactions with other molecules are in their infancy, and more work is still needed.
Research topicsThe potential topics include, but not limited to the following:
- lncRNA detection and biomarker discovery
- CLIP-Seq and RIP-Seq data analysis
- Prediction of physical binding between lncRNA and DNA, RNA and protein.
- Competition and interaction between lncRNA, miRNA and mRNA
- Studying methylation regulating lncRNA functions
- Function Prediction for lncRNAs
- Deep learning approaches to lncRNA/RNA binding protein prediction
- Computational approaches to analyzing lncRNA
- lncRNA 3D secondary structures
- lncRNA-protein interactions
- lncRNA in epigenetic regulation
- lncRNA associated diseases network
- lncRNAs in plant genomics
- lncRNAs in phenotype-genotype problems
- CRISPR/Cas9 and Genome editing in lncRNAs
We invite you to submit papers with unpublished, original research describing recent advances on the areas related to this workshop. Submissions could be full papers (up to 8 pages), short papers (2 pages), or a 1-page abstract. Submissions will undergo peer review by the conference program committee. All papers or abstracts accepted will be included in the Workshop Proceedings published by the IEEE Computer Society Press and will be available at the workshop. Authors of selected submissions will be invited to extend their papers for submission to a special issue in a reputable journal. For each accepted submission, one student author (or postdoc) will be provided a complimentary registration.
Funds are available for limited fellowships to support students and researchers / participants from underrepresented minority groups.
(Abstract, Short Paper, or Full Paper)Please submit your abstract (1 page), short paper (2 pages), or full-length paper (up to 8 pages in IEEE 2-column format) through the online submission system. Electronic submissions in pdf format are required. Click on this link to submit paper.
Submitted papers will be judged for poster or oral presentation.
- Nov 4, 2020 11:59:59 PM WST: Due date for full workshop paper submission.
- Nov 17, 2020: Notification of paper acceptance to authors
- Nov 26, 2020: Camera-ready of accepted papers
- Dec 16-19, 2020: Workshops
Workshop RegistrationWorkshop registration is through the main IEEE BIBM conference website. Information about registration and registration cost are available at the indicated link.
Registration will be for the main conference, which includes workshop attendance. To receive relevant information about the workshop program, please email workshop organizers at firstname.lastname@example.org after you register for the conference.
- Linking RNA to Chromatin by John Rinn
- Hunting for therapeutic long noncoding RNAs by Rory Johnson
- Oncogenic lncRNA identification on the basis of epigenetic code by Kaifu Chen
The program plan for the workshop can be found here
KEYNOTE: Linking RNA to ChromatinABSTRACT
The non-protein coding portions of the human genome, or the noncoding genome, is a bizarre, confusing and exciting aspect of our genetic template. The sequencing of the human genome opened the wardrobe to Narnia, filled with fascinating new regulatory elements and molecular modalities. Here we will discuss our journey into “noncodarnia” and what we have found in the wardrobe over the past 15 years.
John Rinn - Leslie Orgel and Marvin Caruthers Professor of RNA Science at the University of Colorado Boulder. In late 2017, John Rinn moved from Harvard University and the Broad Institute to the University of Colorado Boulder. His laboratory aims to understand how the noncoding (non protein coding) genome regulates development and disease. This led to early discoveries that the genome encodes a mysterious class of RNA genes termed long noncoding RNAs (lncRNA). The Rinn laboratory research has spent decades identifying and mapping lncRNA loci across many species with a parallel goal of assessing how these newly identified lncRNAs contribute to cellular and organismal phenotypes.
Prior to CU Boulder, John Rinn served as a tenured professor at Harvard University. The previous research by the Rinn laboratory at was carried out at Harvard University department of Stem Cell and Regenerative Biology (HSCRB), the Broad Institute and Beth Israel Deaconess Medical Center (BIDMC) at Harvard Medical School. This genome wide research honed in on a small set of lncRNAs that exhibit bona fide RNA based mechanisms and some with genetic associations to human disease.
These findings culminated in the need to understand a new a fundamental question: how do these "RNA Machines" work on a molecular level?
It was this question that lead the Rinn lab to move from Harvard to CU Boulder. In addition to research Professor Rinn has a long standing passion for teaching with development of graduate level RNA genomics courses to sophomore biology at Harvard that blends the fundamentals of biology with modern genomic approaches. This was another motivation to move to CU Boulder BioFrontiers that is based in integrative biology and an exciting new approach to graduate school education.
John Rinn earned his bachelor’s degree in chemistry from the University of Minnesota. He graduated cumma sum laude with department honors, earned the 1999 Casmir Ilenda Award for the university’s best senior thesis research and presentation. He went on to obtain his doctoral degree in biophysics and biochemistry from Yale University, where earned the 2008 Damon Runyon Cancer Foundation Postdoctoral Scholarship with Howard Chang at Stanford University.
KEYNOTE: Hunting for therapeutic long noncoding RNAsABSTRACT
Tumours evolve through somatic mutations that enable cells to replicate uncontrollably and invade new sites. Genes carrying these “driver” mutations are prime therapeutic targets, and hundreds of protein-coding driver genes have been identified through targeted sequencing of their exons. Unfortunately, the lack of entire tumour genome sequences has made it impossible to search for driver elements in the noncoding genome, including the many thousands of long noncoding RNAs (lncRNAs). Very recently, this has been solved by the International Cancer Genome Consortium’s “PCAWG” (Pan Cancer Analysis of Whole Genomes) project, which has comprehensively mapped mutations across >2500 tumour genomes. We have developed a bioinformatic pipeline, ExInAtor2, which identifies candidate driver lncRNAs using integrated signatures of positive evolutionary selection. Applying ExInAtor2 to thousands of primary and metastatic tumour genomes, we present a panorama of driver lncRNAs across multiple cancer types. Candidate driver lncRNAs have a series of suggestive and statistically-significant features of genuine disease genes. To further test the notion that lncRNAs can behave as driver genes, we employ CRISPR-Cas9 to directly assay the phenotypic effects of mutations. In summary, analysis of whole tumour genomes opens new vistas in therapeutically targeting lncRNAs.
Rory Johnson received his MSc in Physics and Biophysics from Imperial College in London. Following a PhD thesis on gene regulation in the nervous system, he performed postdoctoral work at the Genome Institute of Singapore, where he learned next generation sequencing and bioinformatics techniques, and became interested in the nascent field of long noncoding RNAs. He moved to the group of Roderic Guigó at the Centre for Genomic Regulation (Barcelona), where he won a Ramón y Cajal fellowship and worked with the GENCODE consortium to develop annotations of long noncoding RNAs. In 2016 he became a Junior PI with the Swiss Centre for Competence in Research “RNA & Disease” and founded the Genomics of Long noncoding RNAs and Disease (GOLD Lab), which is dedicated to developing new therapies based on long noncoding RNAs. In 2019 he was awarded a Future Research Leaders programme grant by Science Foundation Ireland to establish a research programme in CRISPR, cancer and long noncoding RNAs at University College Dublin. More information can be found at www.gold-lab.org
KEYNOTE: Oncogenic lncRNA identification on the basis of epigenetic codeABSTRACT
Cancers result from a set of genetic and epigenetic alterations. Most known oncogenes were identified by gain-of-function mutations in cancer. While could be achieved by analyzing the alternation of protein sequence coded by mRNA, such analysis is hard for lncRNA that does not code protein. We discover broad genic repression domains (BGRD) on chromatin as an epigenetic signature for oncogenes. A BGRD is a widespread enrichment domain of the repressive histone modification H3K27me3 and is further enriched with multiple other repressive marks including H3K9me3, H3K9me2, and H3K27me2. Further, BGRD displays widespread enrichment of repressed cis-regulatory elements. Shortening of BGRDs is linked to derepression of transcription. BGRDs at oncogenes tend to be conserved across normal cell types. Putative tumor-promoting genes and lncRNAs defined using BGRDs are experimentally verified as required for cancer phenotypes of tumor cells. Therefore, BGRDs play key roles in epigenetic regulation of cancer and provide a direction for mutation-independent discovery of oncogenes.
Dr. Chen is a computational biologist interested in computational modeling of cell identity regulation and tumorigenesis. He received PhD degree from the renowned Beijing Institute of Genomics. Thereafter, he joined the Dan L Duncan Cancer Center at Baylor College of Medicine as a postdoctoral fellow. Dr. Chen started his bioinformatics lab as an Assistant Professor in the Cornell University Weill Cornell Medical College at Houston Methodist Hospital, where he further became an Associate Professor and was designated as the founding Director to develop a Center for Bioinformatics and Computational Biology. Dr. Chen is currently an Associate Professor in the Harvard Medical School at Boston Children’s Hospital.
- Don Adjeroh, PhD, Computer Science & Electrical Engineering, West Virginia University (WVU), Morgantown, WV, USA
- Xiaobo Zhou, PhD, School of Medicine, University of Texas Health Systems, Houston, TX, USA
- Ivan Martinez, PhD, Department of Microbiology, Immunology and Cell Biology, WVU School of Medicine, Morgantown, WV, USA
- Leonard Lipovich, PhD, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
Program Committee Members
- Mauro Calabrese, Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, USA
- Jianlin Jack Cheng, Department of Electrical Engineering and Computer Science, University of Missouri - Columbia, USA
- Thomas Derrien, University of Rennes 1, CNRS, IGDR - UMR 6290, Rennes, France
- Jean Gao, Computer Science and Electrical Engineering, University of Texas at Arlington, USA
- David A Hendrix, Depts. of Biochemistry/Biophysics, & Computer Science, Oregon State University, USA
- Bing-Hua Jiang, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, USA
- Rory Johnson, University of Bern, Switzerland
- Claudia Kutter, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden
- Ananda M. Mondal, School of Computing and Information Sciences, Florida International University, USA
- Xinxia Peng, Department of Molecular Biomedical Sciences, North Carolina State University, USA
- Peiqing Sun, Wake Forest School of Medicine, Wake Forest University, USA
- Umesh Reddy, Department of Biology, West Virginia State University, USA
- Mian Wu, School of Life Sciences, University of Science and Technology of China, China
For general inquiry, please send an email to Donald Adjeroh at email@example.com.
Virtual / Online