NERIC 2017 Speakers

Cathy H. Wu, PhD

Cathy H. Wu, PhD

Research Interests

Systems integration is becoming the driving force for the 21st century biology. Researchers are systematically tackling gene functions and complex regulatory processes by studying organisms at different levels of organization, from genomes, transcriptomes and proteomes to metabolomes and interactomes. To fully realize the value of such high-throughput data requires advanced bioinformatics for integration, mining, comparative analysis, and functional interpretation. My group conducts bioinformatics and computational biology research and has developed a bioinformatics resource at the Protein Information Resource with integrated databases and analytical tools to support genomics, proteomics and systems biology research [Wu et al., 2003]. PIR is a member of the UniProt Consortium to provide the central international resource on protein sequence and function [Wu et al., 2006]. The PIR web site and the UniProt web site at PIR are accessible by researchers worldwide with over 4 million hits per month from over 100,000 unique sites.

Our research encompasses protein evolution-structure-function relationships, biological text mining, protein ontology, proteomic bioinformatics, computational systems biology, and bioinformatics cyberinfrastructure. The protein-centric bioinformatics framework we are developing connects data mining, text mining and ontology for functional analysis of genes and proteins in the systems biology context. The integrative approach reveals hidden relationships among the various components of the biological systems, allows researchers to ask complex biological questions and gain better understanding of disease processes, and facilitates target discovery. We will further establish a new Center for Bioinformatics and Computational Biology at University of Delaware to foster collaborative interdisciplinary research and to offer graduate degree programs in Bioinformatics and Computational Biology to train the next generation of researchers and educators.

Current Projects

  • Protein family classification, functional annotation, and structure-function analysis – As a central approach to protein annotation for the UniProt Knowledgebase, we employ a classification-driven rule-based method. The PIRSF system classifies proteins from superfamily to subfamily levels to reflect evolutionary relationship of proteins and their domain architecture, allowing comparative studies of protein function and evolution [Wu et al., 2004; Nikolskaya et al., 2006]. Coupling with manually curated, structure-guided rules, the system supports the standardization and accurate annotation of protein names, functions, and functional sites [Wu et al., 2006]. The systematic approach provides high-quality functional annotation, while keeping pace with the exponential growth of molecular sequence data.
  • Biological text mining – With an ever-increasing volume of scientific literature now available electronically, we have been collaborating with several Natural Language Processing research groups to develop algorithms for text mining and information extraction [Hirschman et al., 2002]. Several projects have led to tools directly accessible from the iProLINK text mining resource [Hu et al., 2004], including the BioThesaurus of gene/protein names that allows the identification of synonymous and ambiguous names [Liu et al., 2006] and the RLIMS-P text mining system to extract phosphorylation information (kinase, protein substrate, and phosphorylation sites) from Medline abstracts [Hu et al., 2005]. We plan to develop a “configurable, intelligent and integrated” text mining system as the link bridging PubMed and databases for knowledge discovery. We co-organize the BioCreative Challenge Evaluations, bringing together both the text mining and biological research communities to evaluate and guide the future development of text mining systems.
  • Biomedical ontology – As biomedical ontologies emerged as critical tools in biological research for semantic integration of complex data in disparate resources, we have developed a Protein Ontology (PRO) in the OBO (Open Biomedical Ontologies) Foundry framework [Natale et al., 2007]. Extending from the evolutionary relationships of protein classes to the representation of multiple protein forms of genes (e.g., isoforms, post-translational modifications), PRO allows precise definition of protein objects in biological context (e.g., pathways, networks, complexes) and specification of relationships with other ontologies (such as Gene Ontology) [Arighi et al., 2009]. The project aims to capture knowledge representation of protein biology embedded in the scientific literature to facilitate pathway, network and disease modeling.
  • Omics data integration and pathway/network analysis – Designed for data integration in a distributed environment, the iProClass database provides rich protein annotation with data from over 100 molecular databases [Wu et al., 2004]. It is also the underlying data warehouse for gene/protein ID and name mapping. Built upon iProClass and UniProt, we have developed the iProXpress system for functional profiling and pathway analysis of large-scale gene expression and proteomic data [Huang et al., 2007]. iProXpress has been applied to several studies, including proteomic profiling of melanosomes and lysosome-related organelle proteomes, identification of signaling pathways and networks underlying estrogen-induced apoptosis of breast cancer cells, and analysis of cellular pathways in radiation-resistant cells [Chi et al., 2006; Hu et al., 2007; 2008]. As part of the NIAID biodefense proteomics program, we have integrated various omics data on pathogens and their hosts, allowing biologists to query and analyze data from multiple disparate proteomic centers about pathogen-host relationships. We have conducted integrative bioinformatics analysis of protein structure, function and evolution to identify potential targets for hemorrhagic viruses [Mazumder et al., 2007]. We plan to further develop network mining, visualization and prediction methods, and coupling with the integrative bioinformatics approach, to facilitate data-driven hypothesis generation.

Agenda

(Information subject to change)

Wednesday, August 16th

2:00 - 9:00 PM Registration Desk Hours of Operation (Diamond Foyer)
5:00 - 6:00 PM Reception and Poster Session I Setup (Emerald Promenade)
6:00 - 6:15 PM Welcoming Remarks (Emerald I-III Ballrooms) Ralph Budd, MD, Director, Vermont Center for Immunology and Infectious Diseases, UVM College of Medicine, Judith Van Houten, PhD,  Director, Vermont Genetics Network, UVM President Thomas Sullivan and UVM Provost David Rosowsky, PhD
6:15 - 7:30 PM Plated Dinner (Emerald I-III Ballrooms)
7:30 - 9:00 PM Poster Session I (Undergraduate students and Cores) (Emerald Promenade)

Thursday, August 17th

COBRE/INBRE Business Grant Managers Meeting with Arina Kramer, Grants Specialist at the Center for Research Capacity Building, NIGMS (Carlton Boardroom)
7:00 AM - 5:30 PM Registration Desk Hours of Operation (Diamond Foyer)
7:00 - 8:15 AM Breakfast, Career Tables for interested students, Poster Session II Set-up (Exhibition Hall)
8:30 - 9:15 AM Opening Remarks (Emerald I-III Ballrooms) NIGMS staff:
9:30 - 10:00 AM Break and Refreshments (Emerald Promenade)
10:00 - 12:00 PM Concurrent Sessions
  1. Core Presentations of resources available to NERIC investigators (about 20 min each, followed by table discussions with individual Core leaders) (Emerald III Ballroom)
    • Eric Kmiec, PhD, Helen F. Graham Cancer Center & Research Institute, Newark, DE
      "CRISPR-based Gene Editing in Biomedical Research"
    • Youngwook Ahn, PhD, Brown University Transgenics and Gene-Targeting Facility
      “CRISPR/Cas9 Mouse Preparation”
    • Bongsup Cho, PhD, Coordinator INBRE and Professor, The University of Rhode Island
      "Expanding Bioinformatic Core: 3D printing of molecules and viruses!”
    • Nagib Ahsan, PhD, Brown University
      "Proteomics Core Facility"
    • Calvin Vary, PhD, Maine Medical Research Institute
      "Lipidomics"
    • Dwight Matthews, PhD, University of Vermont
      "Metabolomics and 13C-labeling"
  2. Entrepreneurship Workshop: how to turn your innovative ideas into reality. (Emerald II Ballroom)
    • Keynote speaker, Mathew Portnoy, PhD, Overall HHS SBIR/STTR Program Manager, NIH Program Manager, NIH Office of Extramural Programs
    • Pitch presentations by IDeA entrepreneurs
    • Mercedes Rincón, PhD,  Associate Professor, Medicine Immunobiology Program, UVM College of Medicine
      "Welcome to the I-Trep program for IDeA states"
    • Three Round tables, topics to choose
  3. INBRE Program (Emerald I Ballroom)
    • 10:00 - 11:00 AM - Sharon O'Connor, MS, MBA, Internal Evaluation Manager, Dartmouth College, New Hampshire INBRE
      "INBRE Program Evaluation"
    • 11:00 - 12:00 PM - Elizabeth Ambos, PhD, Executive Officer, Council on Undergraduate Research
      "PM Council on Undergraduate Research Presentation"
10:30 - 11:30 AM COBRE/INBRE Business Grant Managers Meeting with Arina Kramer, Grants Specialist at the Center for Research Capacity Building, NIGMS (Carlton Boardroom)
12:00 - 1:30 PM Lunch and Networking (Exhibition Hall)

VGN Baccalaureate Partner Institution Meeting (Carlton Boardroom)
1:30 - 3:30 PM Concurrent Scientific Sessions (solicit themes from PIs and from abstracts received). Development/Genetics (Emerald I Ballroom) Chair, Cancer (Emerald III Ballroom) Chair,
  • Featured Speaker: Patrycja Dubielecka, PhD, Brown University
    “Beyond JAK/STAT: Signaling Pathways Contributing to the Pathogenesis of Myeloproliferative Neoplasms”
Infectious Diseases and Immunology (Emerald II Ballroom) Chair, William Green, PhD, Professor of Microbiology and Immunology, Geisel School of Medicine, Dartmouth
3:30 - 3:45 PM Break and Refreshments (Emerald Promenade)
3:45 - 4:45 PM Keynote Lecture I (Emerald III Ballroom)
4:45 - 6:00 PM Poster Session II (Graduate students and Postdoctoral Fellows) (Emerald III Ballroom)
6:00 PM Dinner on your own in Burlington

Friday, August 18th

8:00 - 9:00 AM Breakfast (Exhibition Hall)
9:00 - 10:00 AM Cool ideas from IDeA programs (Emerald III Ballroom)
  • Bruce Stanton, PhD, Professor of Microbiology and Immunology, Geisel School of Medicine, Dartmouth
    “Leveraging COBRE Resources with Philanthropy”
  • Marie Stuart, MD, PI of SCD COBRE Program, Director of Hematology Research A.I. DuPont Hospital for Children
    “Single Disease Centered COBREs…A Novel Approach”
  • W. Kelley Thomas, PhD, Professor, Dept. Molecular, Cellular and Biomedical Sciences, University of New Hampshire
    “Early Undergraduate Experiences in Bioinformatics”
10:00 - 12:00 PM Concurrent Scientific Sessions Neuroscience (Emerald I Ballroom) Chair, Judith Van Houten, PhD
  • Featured Speaker: Matthew E. R. Butchbach, PhD, University of Delaware
    "Characterization of Small Molecule Neuroprotectants for Spinal Muscular Atrophy”

Cardiovascular and Pulmonary Systems (Emerald III Ballroom) Chair, Bruce Stanton, PhD

Bioinformatics, Computational Biology, Complex Systems (Emerald II Ballroom) Chair, Cathy Wu, PhD, Edward G. Jefferson Chair of Bioinformatics & Computational Biology, University of Delaware
  • Featured Speaker: Benjamin King, PhD, University of Maine
  • Featured Speakers: Dr. Malcolm D’Souza and Dr. Derald Wentzien from Delaware INBRE Wesley College
    “Undergraduate Data Science Research Projects Form an Integral Component of the Wesley College Science and Mathematics Curriculum”
12:00 - 1:00 PM Lunch and Networking Box lunches (G's Restaurant)
1:00 PM Conference Concludes