Bioinformatics Research and Training at UTEP

The University of Texas at El Paso

College of Science

Bioinformaticswww.bioinformatics.utep.edu

Professor, Department of Mathematical Sciences and Professor, Department of Mathematical Sciences and Director, Bioinformatics and Computational Science ProgramsDirector, Bioinformatics and Computational Science Programs

Director, Bioinformatics Core FacilityDirector, Bioinformatics Core FacilityBorder Biomedical Research Center (BBRC) Border Biomedical Research Center (BBRC)

The University of Texas at El Paso, El Paso, TexasThe University of Texas at El Paso, El Paso, Texas

Ming-Ying Leung, Ph.D.Ming-Ying Leung, Ph.D.

Bioinformatics Program

The University of Texas at El Paso

College of Science

Bioinformaticswww.bioinformatics.utep.edu

Interdisciplinary program supported by departments of Biological SciencesChemistryComputer ScienceMathematical Sciences

With 24 faculty and staff members from the Colleges of Science, Engineering, and Health Sciences.

Biological Sciences:Biological Sciences: Steve Aley, Igor Almeida, Sid Das, Steve Aley, Igor Almeida, Sid Das, Krinstine Garza, Kyle Johnson, Carl Lieb, Vanessa Krinstine Garza, Kyle Johnson, Carl Lieb, Vanessa Lougheed, Elizabeth Walsh, Jianying ZhangLougheed, Elizabeth Walsh, Jianying Zhang

Chemistry:Chemistry: James Becvar, Ricardo Bernal, Mahesh James Becvar, Ricardo Bernal, Mahesh Narayan, Chuan XiaoNarayan, Chuan Xiao

Clinical Laboratory ScienceClinical Laboratory Science:: Delfina Dominguez Delfina Dominguez

Computer Science:Computer Science: Martine Ceberio, Olac Fuentes, Martine Ceberio, Olac Fuentes, Vladik Kreinovich, Vladik Kreinovich,

Electrical and Computer Engineering:Electrical and Computer Engineering: Wei QianWei Qian

Mathematical Sciences:Mathematical Sciences: Art Duval, Hamide Dogan, Art Duval, Hamide Dogan, Ming-Ying Leung, Naijun ShaMing-Ying Leung, Naijun Sha

Staff:Staff: Oliana Alikaj, Gerardo CardenasOliana Alikaj, Gerardo Cardenas33

Bioinformatics Faculty and Staff

Program GoalsProgram Goals

1. Training1. TrainingNSF-Funded Undergraduate Participation NSF-Funded Undergraduate Participation in Bioinformatics Training (UPBiT)in Bioinformatics Training (UPBiT)

Professional Science Master (PSM) Professional Science Master (PSM) degree in Bioinformatics degree in Bioinformatics

Computational Bioscience for Ph.D. in Computational Bioscience for Ph.D. in Computational ScienceComputational Science

Program GoalsProgram Goals

2. Research2. ResearchBiomolecular Sequence AnalysisBiomolecular Sequence Analysis

Ecoinformatics and Phylogenetics Ecoinformatics and Phylogenetics

Medical Imaging InformaticsMedical Imaging Informatics

Molecular Structure and DynamicsMolecular Structure and Dynamics

Proteomics Data AnalysisProteomics Data Analysis

Students and Graduates Students and Graduates

Current students and trainees: Current students and trainees: 16 Undergrad trainees in UPBiT, 16 M.S. , and 4 Ph.D. students 16 Undergrad trainees in UPBiT, 16 M.S. , and 4 Ph.D. students

in computational bioscience.in computational bioscience.

Students and Graduates Students and Graduates

Over 50 graduates working at:Over 50 graduates working at:• Academic Institutions (e.g., Stanford, Vanderbilt, Texas Tech., UTEP)Academic Institutions (e.g., Stanford, Vanderbilt, Texas Tech., UTEP)• Research Labs (e.g., Broad Inst., Whitehead Inst., M.D. Anderson) Research Labs (e.g., Broad Inst., Whitehead Inst., M.D. Anderson) • Government agencies (e.g., NIH, USDA, USAMRIID)Government agencies (e.g., NIH, USDA, USAMRIID)

• Industry (Pfizer, MonsantoIndustry (Pfizer, Monsanto))

Ecoinformatics and Phylogenetics

Molecular Structure and

Dynamics

Biomolecular Sequence Analysis

Microarray and Proteomics Data

Analysis

ResearchRotations

2

1

M

ii

C

2|| ||Q(w)w

Undergraduate Participation in Bioinformatics Training (UPBiT)Undergraduate Participation in Bioinformatics Training (UPBiT)

NIH-Funded Bioinformatics Core Facility in theNIH-Funded Bioinformatics Core Facility in theBorder Biomedical Research Center (BBRC)Border Biomedical Research Center (BBRC)

DNA Analysis

Cell Culture

Biomolecule Analysis

Analytical Cytology

Statistical Consulting Lab

Integrate Computational &

Experimental Approachese.g., RNA

structure prediction

Statistical Bioinformatics

Study Design & Data Analysis

Bioinformatics Computing Lab

e.g., data

mining

BBRC Bioinformatics Core FacilityBBRC Bioinformatics Core Facility

• Bioinformatics Computing LabBioinformatics Computing Lab• Translational Bioinformatics Lab Translational Bioinformatics Lab • Structural Bioinformatics LabStructural Bioinformatics Lab

Provide bioinformatics support to biomedical research:Provide bioinformatics support to biomedical research:

Supporting BBRC research clusters throughSupporting BBRC research clusters through computational computational modeling, data management and interpretations, to final modeling, data management and interpretations, to final production of and dissemination bioinformatics toolsproduction of and dissemination bioinformatics tools..

Interfacing with other BBRC core facilities by establishing Interfacing with other BBRC core facilities by establishing protocols and operation manuals integrating computational protocols and operation manuals integrating computational components in the experimental procedure.components in the experimental procedure.

Providing consulting services for non-BBRC researchers, Providing consulting services for non-BBRC researchers, strengthening collaborative efforts for interdisciplinary strengthening collaborative efforts for interdisciplinary research in the border region.research in the border region.

Specific Aims for Bioinformatics Core Facility

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1212

Computing Resources Development Plan

Connection with Other BBRC UnitsConnection with Other BBRC Units

1313

RNAVLab: Virtual laboratory for RNA sequence analysis and RNAVLab: Virtual laboratory for RNA sequence analysis and secondary structure prediction (with DNA sequencing core)secondary structure prediction (with DNA sequencing core) RNASSA: RNA Secondary Structure AnalysisRNASSA: RNA Secondary Structure Analysis InversFinder: Finding inversionsInversFinder: Finding inversions Segmenta: RNA SegmentationSegmenta: RNA Segmentation Grid and Cloud ComputingGrid and Cloud Computing

Post-translational modification studies (with Biomolecular Post-translational modification studies (with Biomolecular Characterization Core) Characterization Core) GPI and GPI-anchored protein structure prediction based on mass GPI and GPI-anchored protein structure prediction based on mass

spectrometry data (in collaboration with Dr. Clemente Aguilar, spectrometry data (in collaboration with Dr. Clemente Aguilar, National Institute of Mathematical and Biological Synthesis)National Institute of Mathematical and Biological Synthesis)

ISOGlyP (Isoform Specific O-Glycosylation Prediction) ISOGlyP (Isoform Specific O-Glycosylation Prediction) (with Dr. Thomas Gerken as PI, submitted R01 in January 2014)(with Dr. Thomas Gerken as PI, submitted R01 in January 2014)

Software Development

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Glycosylation Site Prediction Software (isoglyp.utep.edu)

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Establish a standard toolset on Bioinformatics GridEstablish a standard toolset on Bioinformatics Grid to facilitate the workflow for computational prediction to facilitate the workflow for computational prediction of protein structures, interactions, and docking models.of protein structures, interactions, and docking models.

Current BBRC projects include:Current BBRC projects include: Searching for cancer-related interactorsSearching for cancer-related interactors for tumor- for tumor-

associated antigens from Human Protein Reference associated antigens from Human Protein Reference Database (HPRD) and other sources. Database (HPRD) and other sources.

In silico In silico design of nociceptin agonists design of nociceptin agonists for Post-Traumatic for Post-Traumatic Stress Disorder (PTSD) through halogen bonding. Poster to Stress Disorder (PTSD) through halogen bonding. Poster to be presented by Dr. Mahesh Narayan at the Advancing be presented by Dr. Mahesh Narayan at the Advancing Computational Biology @ Howard University Symposium.Computational Biology @ Howard University Symposium.

Protein Structure, Dynamics and Interactions

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1717

Motif detection to identify potential enhancer Motif detection to identify potential enhancer elements critical for learning and memory elements critical for learning and memory (led (led by Dr. K. Han)by Dr. K. Han)

GPCR prediction and vaccine development GPCR prediction and vaccine development (Collaboration with Dr. Felix Guerrero of the USDA-(Collaboration with Dr. Felix Guerrero of the USDA-ARS and Dr. Kyle Johnson, funded by the USDA-HSI ARS and Dr. Kyle Johnson, funded by the USDA-HSI Program)Program)

Functional genomic analysis of high-risk Functional genomic analysis of high-risk childhood leukemia childhood leukemia (BBRC pilot project, led by (BBRC pilot project, led by Dr. Jeremy Ross)Dr. Jeremy Ross)

1818

Sequence Analysis Projects

1919

2020

2121

Relevance to Health Disparities: Hispanic children have the highest rates of incidence and death from acute lymphoblastic leukemia (ALL) in the U.S.

Pilot Project: Functional Genomic Analysis of Pilot Project: Functional Genomic Analysis of High-Risk Childhood LeukemiaHigh-Risk Childhood Leukemia

Major Objective: Provide significant insight into the genetic abnormalities driving ALL tumor cell growth and drug resistance in the Hispanic population.Approach: 1) Identify protein-encoding somatic mutations using whole-exome sequencing of DNA isolated from an Hispanic pediatric leukemia patient cohort of new onset or relapsed ALL. 2) Develop and employ a pathway-based computational pipeline to prioritize functionally relevant sequence variants and aid biological interpretation.

Project Highlight - BBRC “OncoMiner” Pipeline

Continue to strengthen bioinformatics supportContinue to strengthen bioinformatics support to genomics to genomics and proteomics data analysis.and proteomics data analysis.

Expand software development capabilities Expand software development capabilities for biomedical for biomedical informatics and translational bioinformatics research.informatics and translational bioinformatics research.

Create portals from Bioinformatics GridCreate portals from Bioinformatics Grid to high to high performance computing platforms at UTEP and TACC, and performance computing platforms at UTEP and TACC, and the RTRN Data Coordinating Center.the RTRN Data Coordinating Center.

Explore further training and professional opportunities Explore further training and professional opportunities for students and graduates of the programfor students and graduates of the program

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Future Plan

Email: Email: bioinformatics@utep.edu

Web: Web: www.bioinformatics.utep.edu

Facebook: Facebook: www.facebook.com/Bioinformatics.UTEP

Phone: 915.747.8484Phone: 915.747.8484

The University of Texas at El Paso

College of Science

Bioinformaticswww.bioinformatics.utep.edu

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