Click here for the workshop program.
- Mauro Calabrese, PhD (MIT), Department of Pharmacology, University of North Carolina, Chapel Hill, NC
- Lynne Maquat, PhD (UW-Madison) , University of Rochester Medical Center, University of Rochester, NY
Keynote Title: "K-mer based sequence comparison as a way to identify functional lncRNAs"
Abstract: The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence similarity; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method called SEEKR that deconstructs linear sequence relationships in lncRNAs to evaluate similarity based on the abundance of short motifs called k-mers. Using SEEKR, we found that lncRNAs of related function often have similar k-mer profiles despite lacking linear similarity, and that k-mer profiles can correlate with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. Moreover, at the level of k-mers, we found that Xist shares a substantial level of regional similarity to its putative functional analogue, the marsupial lncRNA Rsx. Our data demonstrate that even in situations where BLAST-like alignments may fail to detect meaningful biological trends, k-mer-based sequence comparisons can succeed. We are currently developing an approach to k-mer-based comparison that utilizes a hidden Markov model, which may prove useful when scanning genomes and transcriptomes for lncRNAs of functional significance.
Keynote-2 Title: "3'UTR-Mediated Post-transcriptional Effects on Human Gene Expression via Staufen and SINEs"
Abstract: Primate-specific Alu SINEs, as well as rodent-specific B and ID (B/ID) SINEs, can promote mRNA export from the nucleus to the cytoplasm, translation in the cytoplasm and/or Staufen-mediated mRNA decay (SMD) when present in mRNA 3'-untranslated regions (3'UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with the double-stranded RNA-binding protein Staufen (STAU), and their rapid divergence in different evolutionary lineages suggest they have generated substantial modification of post-transcriptional gene-control networks during mammalian evolution. This, coupled with the fact that most mammalian genes express mRNA isoforms with distinct 3'UTRs through alternative cleavage and polyadenylation has led to a complex post-transcriptional regulatory network. This network will be discussed.
Call for Papers
IEEE BIBM 2019 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 2019) to be held in November 2019, in conjunction with IEEE BIBM 2019 conference in San Diego, CA, USA.
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. 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.
Research topicsThe potential topics include, but not limited to the following:
- ncRNA detection and biomarker discovery
- CLIP-Seq and RIP-Seq data analysis
- Prediction of physical binding between lncRNA and DNA, RNA and protein.
- Understanding the competition 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 special issues in prestigious journals.
Funds are available for limited travel fellowships to support students and researchers from underrepresented minority groups.
LncRNA Annotation Challenge Competitions
To further enhance community building and interaction, the Workshop will include a session on crowd-sourced LncRNA competitions or challenges that engage community members. Results and awards related to these annotation challenge sessions will be presented at the Workshop. Click here for more details on the challenge.
Paper SubmissionPlease submit a full-length paper (up to 8 page IEEE 2-column format), short paper (2 pages), or abstract (1 page) through the online submission system. Electronic submissions in pdf format are required.
- Sep 20 Oct 8, 2019 11:59:59 PM EST: New due date for paper submission.
- Oct 15 Oct 20, 2019: Notification of paper acceptance
- Nov 1, 2019: Camera-ready version of accepted papers
- Nov 18-21, 2019: Workshops
- Don Adjeroh, PhD, Computer Science & Electrical Engineering, West Virginia University (WVU)
- Xiaobo Zhou, PhD, School of Medicine, University of Texas Health Systems, Houston, TX
- Ivan Martinez, PhD, Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine
- Rory Johnson, University of Bern, Switzerland
Program Committee Members
- Jianlin Jack Cheng, Department of Electrical Engineering and Computer Science, University of Missouri - Columbia, USA
- Thomas Derrien, University of Rennes 1, France
- Claudia Kutter, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden
- Jean Gao, Computer Science and Electrical Engineering, University of Texas at Arlington, USA
- Bing-Hua Jiang, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, USA
- Rory Johnson, University of Bern, Switzerland
- Leonard Lipovich, Center for Molecular Medicine and Genetics, Wayne State University, USA
- Han Liang, Dept. Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, USA
- Hui-Kuan Lin, Wake Forest Baptist Medical Center, Wake Forest University, USA
- Ana Claudia Marques, Department of Computational Biology, Universite de Lausanne, Switzerland
- 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.
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