PANEL SESSION

CALL FOR PAPERS

Submission deadline: August 1st, 2017

CALL FOR ABSTRACTS

Submission deadline: November 13th, 2017

Pacific Symposium on Biocomputing

January 3-7, 2018
Fairmont Orchid Resort
The Big Island of Hawai'i

MOTIVATION

It remains difficult to assign functional mechanisms to variation in intergenic and/or noncoding DNA, even in cases where these can be confidently associated with variation of a biological trait. Altered regulatory activity is the most commonly considered candidate, but identifying the most relevant relationships or functions in the absence of an a priori biological hypothesis requires the intersection of big data, computing, and creativity.

Multiple reports have linked regions of noncoding DNA to biological functions, traits, and diseases (GWAS and others) (1). Independently, an abundance of biological evidence (ENCODE and others) has highlighted a variety of biochemical activities within regions of noncoding DNA. Despite the vast quantities of data being generated, there remains a gap in connecting these at a genome-wide or systems scale beyond one-to-one candidate positional overlap, descriptive statistics, or similar.

Thus, there arises a unique opportunity for computational biologists to identify network and systems properties of noncoding DNA, linking evidence from biochemical assays, genetics, and evolutionary biology with other datasets. These can predict downstream biology, functional convergence (2), and impacted mechanisms that ultimately lead to disease. In addition to novel basic science insights, understanding the mechanisms perturbed by variation in noncoding DNA can implicate new pathophysiological mediators and unveil new therapeutic targets (3).

Advances in experimental and analytical techniques together with large-scale data collection have substantially expanded the range of perspectives implicating noncoding DNA elements and loci with functional activity. Examples include:

  • ChIP-Seq
  • Sono-Seq
  • ATAC-Seq
  • ChIA-PET
  • ChIP-PET
  • DNA-PET
  • ChiRP-Seq
  • eQTL
  • ChIP-nexus
  • DRIP-seq
  • ChIP-exo
  • Competition-ChIP
  • eWAS
  • Ultraconserved elements (UCE)

TOPICS OF INTEREST

  • Biomolecular mechanisms disrupted by variation in non-transcribed, non-promoter disease-associated loci
  • Trans-acting retrotransposon activity
  • Biomolecular mechanisms underpinning synergy or antagony between interactions of noncoding Loci
  • Drug repositioning targeting proteins of coding genes regulated by trans-acting ncDNA
  • Pseudogene-associated pathogenecity
  • Systems/network properties of lincRNAs regulating disease-specific miRNA and mRNAs

SUBMISSION

The core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. All accepted papers will be published electronically and indexed in PubMed, and the best of these will be presented orally to the entire conference. PSB will also initiate submission to PubMed Central (PMC); however, PMC indexing applies only to papers that comply with the NIH Public Access Policy.

Researchers wishing to present their research without official publication are encouraged to submit a one-page abstract by the abstract deadline listed below to present their work in the poster sessions.

Please follow paper submission guidelines outlined here

For pre-prints of PSB papers, please make sure to acknowledge PSB and WSP per WSP's guidelines.

Preprint of an article submitted for consideration in the Pacific Symposium on Biocomputing © 2018 World Scientific Publishing Company

ORGANIZERS

Yves A. Lussier, MD, FACMI

Yves A. Lussier, MD, FACMI
Maricel G. Kann, PhD

Maricel G. Kann, PhD
Jason H. Moore, PhD, FACMI

Jason H. Moore, PhD, FACMI
Kenneth S. Ramos, MD, PhD

Kenneth S. Ramos, MD, PhD
Joanne Berghout, PhD

Joanne Berghout, PhD
Francesca Vitali, PhD

Francesca Vitali, PhD

KEY DATES

August 1

  • Paper submissions deadline
  • Travel award applications available

September 5

  • Paper acceptance due to PSB organizers

September 15

  • Notification of paper acceptance

October 2

  • Final paper deadline
  • Deadline for travel award applications

November 13

  • Poster abstract submission deadline
  1. Edwards SL, Beesley J, French JD, Dunning AM. Beyond GWASs: illuminating the dark road from association to function. Am J Hum Genet. 2013;93(5):779-97. doi: 10.1016/j.ajhg.2013.10.012. PubMed PMID: 24210251; PMCID: PMC3824120.
  2. Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. Haiquan Li, Ikbel Achour, Lisa Bastarache, Joanne Berghout, Vincent Gardeux, Jianrong Li, Younghee Lee, Lorenzo Pesce, Xinan Yang, Kenneth S Ramos, Ian Foster, Joshua C Denny, Jason H Moore, Yves A Lussier NPJ GENOMIC MEDICINE
  3. Amorim M, Salta S, Henrique R, Jeronimo C. Decoding the usefulness of non-coding RNAs as breast cancer markers. J Transl Med. 2016;14:265. doi: 10.1186/s12967-016-1025-3. PubMed PMID: 27629831; PMCID: PMC5024523.
For more information, please contact Dr. Colleen Kenost at ckenost@email.arizona.edu
Lussier Lab

Yves A. Lussier, MD

Professor of Medicine
Executive Director of the Center for Biomedical Informatics and Biostatistics
Associate Director for Precision Medicine and Oncoinformatics, UA Cancer Center
Associate Director for Informatics, BIO5 Institute
Associate Vice President for Health Data Sciences
The University of Arizona
yves@email.arizona.edu

Yves A. Lussier is a leader in translational bioinformatics, actively involved with the development of the field and its conferences (PSB session co-chairs x2, co-founder and chair of the AMIA Summit on Translational Bioinformatics and of the Translational Bioinformatics Conference). Recently, his research group computationally predicted antagony between noncoding DNA (disease risk polymorphisms) located in distinct chromosomes that paradoxically interact to reduce the risk of Alzheimer’s Disease and of bladder cancer, which were then confirmed in genome-wide association studies (GWAS) by Jason Moore’s group.

Maricel G. Kann, PhD

Associate Professor of Biological Sciences
University of Maryland, Baltimore County
mkann@umbc.edu

Maricel G. Kann is a leader in translational computational biology and has been actively involved in organizing PSB scientific sessions for over a decade (2006, 2007, 2008, 2013, 2016). Her research interest lies on computationally determining the mechanisms of complex biological processes that underpin healthy vs. diseased organisms. Dr. Kann has developed a unique expertise in accurately predicting protein domain interactions and consequent drug development.

Jason H. Moore, PhD, FACMI

Edward Rose Professor of Informatics
Director of the Institute for Biomedical Informatics
Associate Dean for Informatics of the Perelman School of Medicine
Director of the Division of Informatics, Dept. of Biostatistics and Epidemiology
The University of Pennsylvania
jhmoore@upenn.edu

Jason H. Moore’s research focuses on using informatics methods for identifying combinations of DNA sequence variations and environmental factors that are predictive of human health and complex disease. He and Marylyn Ritchie developed the multifactor dimensionality reduction (MDR) machine learning method for detecting and characterizing combinations of attributes or independent variables that interact to influence a dependent or class variable. He then applied MDR for improved understanding of the interplay of multiple genetic polymorphisms of complex traits in GWAS. Recently, in collaboration with Yves Lussier, he validated in GWAS computational predictions of antagony between noncoding DNA (disease risk polymorphisms) located in distinct chromosomes that paradoxically interact to reduce the risk of Alzheimer’s Disease and of Bladder Cancer.

Kenneth S. Ramos, MD, PhD

Professor of Medicine
Interim Dean of the UA College of Medicine – Phoenix
Executive Director of The Center for Applied Genetics and Genomic Medicine
Associate Vice President for Precision Health Sciences
The University of Arizona
ksramos@email.arizona.edu

Kenneth S. Ramos was inducted into the National Academy of Medicine in 2015 for his pioneering work in understanding the expand mechanisms of long interspersed nuclear elements (LINE1) retrotransposon activity and its contribution to pathophysiology. He is deeply committed to initiatives that advance modern technological applications to improve the quality of health care and reduce both disease burden and health-associated costs. One of his primary areas of focus in partnership with Banner – University Medical Center is the development of precision-health strategies and approaches to advance health-care delivery and outcomes.

Joanne Berghout, PhD

Research Assistant Professor, Medicine
Center for Biomedical Informatics and Biostatistics
The Center for Applied Genetics and Genomic Medicine
The University of Arizona
jberghout@email.arizona.edu

Joanne Berghout has been research faculty at The University of Arizona since 2016. Her research is centered on using ontologies to discover patterns and new insights from genetic data. Recently, this led to the discovery of convergent regulatory mechanisms for intergenic SNPs associated with complex disease, revealed by 2-locus analysis of GWAS candidate SNPs, eQTL data, and enriched ontology annotations. Dr. Berghout holds a PhD in Biochemistry/Molecular Genetics from McGill University and worked previously as the Outreach Coordinator for the Mouse Genome Informatics database at the Jackson Laboratory.

Francesca Vitali, PhD

Research Assistant Professor, Medicine
Center for Biomedical Informatics and Biostatistics
University of Arizona
francescavitali@email.arizona.edu

Francesca Vitali has been research faculty at The University of Arizona since 2016. Her research focuses on machine learning, network and systems approaches to pharmacogenomics, and drug repositioning. Her PhD and post-doctoral studies, conducted under Dr. Riccardo Bellazzi, led her to extend the flexibility of graph-theoretic approaches for integration of biological knowledge and data, which were applied software tools she developed. In collaboration with Drs. Lussier and Berghout, she is investigating drug repositioning in eQTL networks anchored on noncoding disease-associated polymorphisms.