PROFILES - Connect with RTRN Researchers

Ming-Ying Leung
Title Director of Bioinformatics and Computational Science Programs; Director of Bioinformatics Core, Border Biomedical Research Center
Faculty Rank Professor
Degree Ph.D.
Institution University of Texas at El Paso
Department Mathematical Sciences
Clusters Informatics
Address
Department of Mathematical Sciences
The University of Texas at El Paso
City El Paso
State TX
Postal Code 79968
Telephone (915)747-6836
Fax (915)747-6502
Email
QR Barcode

Narrative icon

  My research focuses on developing probabilistic modeling and computational algorithms for bioinformatics analysis of biomolecular sequence data. In particular, I have developed Markov models, scan statistics, and computational algorithms to identify unusual palindromic patterns in the nucleotide sequences and have applied them to the analysis of genomic sequences of DNA and RNA viruses like the herpesviruses and SARS coronaviruses. I have also been developing efficient computational approaches for predicting secondary structures, including pseudoknots, of long RNA sequences. We have devised methods to circumvent the extremely high demands of memory and computing time in the structure prediction problem by using grid computing technologies available in the UTEP Border Biomedical Research Center Bioinformatics Computing Core Facility, where I serve as director. The research in these projects has resulted in several bioinformatics software packages publicly accessible online (bioinformatics.utep.edu/BCL). With broad research interests and experience in probabilistic modeling, algorithm design, and statistical bioinformatics, I have served as PI and co-PI in various projects for setting up and managing computational facilities for biomedical research and as director of the Bioinformatics and Computational Science Programs for administering graduate research training at UTEP. Over the past 20 years, my research has been funded by NIH, NSF, IBM, and the Texas NHARP in viral genome replication, sequence analysis, and RNA structural prediction with a long record of publication in these areas. In addition, I am involved in several collaborative research projects in identifying protein biomarkers for hepatocellular carcinoma, mammogram image analysis, HIV vaccine development, and pipeline implementation for bioinformatics analysis of exonic sequence variants in cancer-related genes.

Mentorship icon

 
Availability Date:
Tuesday, March 01, 2016

I am currently serving as the director and graduate advisor for the MS Bioinformatics and PhD in Computational Science programs, which involve faculty in 10 different departments in science and engineering. I have been advisor to over 100 MS and 30 PhD students, many of whom have been trained in my research projects funded by NIH, NSF, and USDA and then gone on to professional careers at prestigious institutions like MD Anderson Cancer Center, Lawrence Berkeley National Lab, Stanford University, US Army Medical Research Institute of Infectious Disease, Hewlett Packard, Monsanto, and Pfizer. I have also mentored two postdoctoral fellows in 2005 - 2009, who went on to become faculty at the University of Maryland and software engineer at Amazon. In addition, in the past 10 years, I have been an appointed faculty mentor for three tenure-track faculty members at UTEP. Two of them are tenured full and associate professors now. The third one is an assistant professor who joined UTEP in 2014 and is PI of an NSF grant awarded in 2015. I have also served as a collaborator in several NIH-funded pilot projects with junior faculty as PI.

I am available to mentor as:
Faculty mentor

Contact Information for Mentoring:
mleung@utep.edu

Preferred Methods of Mentoring:
  • Email
  • Online Meetings
  • Phone

Programs, Membership, and Biomedical Research icon

Mentoring Mentor

NIH Awarded Grants icon

  Research projects funded by the National Institutes of Health (NIH), the Centers for Disease Control (CDC), the Food and Drug Administration (FDA), and the Department of Veterans Affairs (VA)

Loading
Please wait
1.
2018HEAD START CONNECTS: INDIVIDUALIZING AND CONNECTS FAMILIES TO FAMILY SUPPORT SERVICESHHSP233201500059I/HHSP233201500059I
2.
2018 EARLY CARE AND EDUCATION LEADERSHIP STUDY (EXCELS)HHSP233201500035I / HHSP23337038T
3.
2018WHAT WORKS CLEARINGHOUSE OF PROVEN AND PROMISING APPROACHES TO MOVE WELFARE RECIPIENTS TO WORKHHSP233201500035I_HHSP23337034T
4.
2018RACIAL AND ETHNIC DISPARITIES IN HUMAN SERVICES ANALYSIS EXECUTION PROJECTHHSP233201500064I_HHSP23337020T
5.
2018ASSESSING MODELS OF COORDINATED SERVICES FOR LOW-INCOME CHILDREN AND THEIR FAMILIESHHSP233201500035I/HHSP23337028T
6.
2018CHILD CARE INTERSTATE BACKGROUND CHECKS (CC-IBACS)HHSP233201500045I
7.
2018MOTHER AND INFANT HOME VISITING PROGRAM EVALUATION, LONG-TERM FOLLOW-UP 2 (MIHOPE-LT2)HHSP233201500059I/ HHSP23337010T
8.
2017EXPLORING THE RELATION BETWEEN POSITIVE BEHAVIOR SUPPORT AND LANGUAGE LEARNING OPPORTUNITIES IN PRESCHOOL CLASSROOMS.90YR0101-01
9.
2017ADDRESSING THE NEEDS OF INFANTS AND TODDLERS EXPOSED TO MALTREATMENT: EXAMINING THE IMPACT OF AN INTEGRATED EARLY HEAD START & CHILDREN AND YOUTH SERVICES PROGRAM90YR0102-01
10.
2017LEVERAGING HOME LANGUAGES TO PROMOTE EXECUTIVE FUNCTIONING90YR0103-01
11.
2017A STRENGTHS-BASED APPROACH TO EXAMINING SUPPORTS FOR SELF-REGULATION SKILLS OF LATINO CHILDREN RAISED IN POVERTY90YR0104-01
12.
2017OBSERVING SELF-REGULATION IN CONTEXT IN HEAD START CLASSROOMS AND DUAL LANGUAGE LEARNERS SCHOOL READINESS90YR0105-01
13.
2017IMPLEMENTATION AND ASSESSMENT OF COMPETENCIES FOR TEACHERS AND CAREGIVERS SERVING INFANTS AND TODDLERSHHSP233201500035I/HHSP23337021T
14.
2017ASSESSMENT AND MAPPING OF COMMUNITY CONNECTIONS IN HOME VISITING (AMC-HV)HHSP233201500034I/HHSP23337002T
15.
2017CHILD MALTREATMENT INCIDENCE DATA LINKAGES (CMI DATA LINKAGES)HHSP233201500035I/HHSP23337022T
16.
2017EVIDENCE BUILDING IN TANF: ADVANCING INNOVATIONS TO PROMOTE EMPLOYMENT AND ECONOMIC SECURITY FOR LOW-INCOME INDIVIDUALSHHSP233201500059I/HHSP23337006T
17.
2017HEAD START FAMILY AND CHILD EXPERIENCES SURVEY (FACES) 2019HHSP233201500035I/HHSP23337024T
18.
2016TWO-GENERATION APPROACHES TO IMPROVING FAMILY SELF-SUFFICIENCYHHSP233201500035I/HHSP23337003T
19.
2016BUILDING CAPACITY TO EVALUATE INTERVENTIONS FOR YOUTH/YOUNG ADULTS WITH CHILD WELFARE INVOLVEMENT AT-RISK OF HOMELESSNESS: PHASE IIHHSP233201500035I/HHSP23337013T
20.
2016PROFESSIONAL DEVELOPMENT TOOLS TO IMPROVE THE QUALITY OF INFANT AND TODDLER CAREHHSP233201500035I/HHSP23337007T
21.
2016ASSESSING THE EVIDENCE: HOME VISITING EVIDENCE OF EFFECTIVENESSGS-10F-0050L/HHSP233201500115G
22.
2016TRIBAL HOME VISITING EVALUATION INSTITUTEGS-10F-0204K/HHSP233201500114G
23.
2016FAMILY SELF-SUFFICIENCY DATA CENTER90PD0272-04
24.
2016EVALUATION OF GOAL-DIRECTED PSYCHOLOGICAL CAPITAL AND EMPLOYER COACHING IN HEALTH PROFESSION OPPORTUNITY DEVELOPMENT90HG1003-01
25.
2016CULTURE OF CONTINUOUS LEARNING PROJECT: A BREAKTHROUGH SERIES COLLABORATIVE FOR IMPROVING CHILD CARE AND HEAD START QUALITYHHSP233201500034I/HHSP23337001T
26.
2016DOMESTIC HUMAN TRAFFICKING AND THE CHILD WELFARE POPULATIONHHSP23320150039I/HHSP23337011T
27.
2016EVALUATION OF COACHING-FOCUSED INTERVENTIONS FOR HARD-TO-EMPLOY TANF CLIENTS AND OTHER LOW-INCOME POPULATIONSHHSP233201500035I/HHSP23337018T
28.
2016EVALUATION OF THE NATIONAL HUMAN TRAFFICKING HOTLINE PROGRAMHHSP233201500039I/ HHSP23337007T
29.
2016MULTI-SITE IMPLEMENTATION EVALUATION OF TRIBAL HOME VISITING (MUSE)HHSP233201500133I/HHSP23337004T
30.
2016VARIATIONS IN IMPLEMENTATION OF QUALITY INTERVENTIONS: EXAMINING THE QUALITY-CHILD OUTCOMES RELATIONSHIP IN CHILD CARE AND EARLY EDUCATION (VIQI)HHSP233201500059I/HHSP23337002T
31.
2016DESIGN OPTIONS FOR HOME VISITING EVALUATION (DOHVE) 2.0HHSP233201500133I/HHSP23337002T
32.
2016ADVANCING WELFARE AND FAMILY SELF-SUFFICIENCY RESEARCH PROJECT (FOLLOW-ON) HHSP233201500035I/HHSP23337017T
33.
2016HPOG UNIVERSITY PARTNERSHIPS 2.0 RESEARCH SUPPORTHHSP233201500071I/HHSP23337011T
34.
2015THE CHANGING LANDSCAPE OF PUBLICLY-FUNDED CENTER-BASED CHILD CARE: 1990 AND 2012.90YE0165-01
35.
2015SUBSIDY UTILIZATION AND IMPACT ON EARLY CARE AND EDUCATION OF LOW-INCOME CHILDREN WITH SPECIAL NEEDS90YE0166-01
36.
2015PROMOTING SOCIAL COMPETENCE IN ECE: PREDICTING THE DEVELOPMENT OF PROSOCIAL BEHAVIOR FROM EARLY EXPERIENCES IN CHILD CARE AND FAMILIES90YE0168-01
37.
2015THE IMPACT OF EARLY CARE AND EDUCATION IN CHILD NUTRITION, SEDENTARY BEHAVIOR AND OBESITY BY KINDERGARTEN90YE0170-01
38.
2015HOW PARENTAL PREFERENCES AND SUBSIDY RECEIPT SHAPE IMMIGRANT FAMILIES? CHILD CARE CHOICES90YE0171-01
39.
2015SUPPORTING LOW-INCOME FAMILIES: STATE VARIATIONS IN CHILD CARE SUBSIDIES AND TANF POLICIES AND CHILDREN'S DEVELOPMENTAL ECOLOGIES90YE0173-01
40.
2015MITIGATING SUSCEPTIBILITY WITH THE CHILD CARE DEVELOPMENT FUND: USING FOUR LARGE DATA SETS TO CLASSIFY RISK PROFILES AND RISK TRANSMISSION BY MODIFIABLE FACTORS90YE0175-01
41.
2015ARE HIGHER SUBSIDY PAYMENT RATES AND PROVIDER-FRIENDLY PAYMENT POLICIES ASSOCIATED WITH CHILD CARE QUALITY?90YE0177-01
42.
2015CHILD CARE FACTORS THAT INFLUENCE PARENTAL ENGAGEMENT: UNDERSTANDING LONGITUDINAL PATHWAYS TO CHILDREN?S SCHOOL READINESS90YE0178-01
43.
2015CONSTELLATIONS OF SUPPORT: TEACHER PROFESSIONAL DEVELOPMENT IN HEAD START AND CHILD OUTCOMES90YE0179-01
44.
2015SUHMRE: SAME-SEX RELATIONSHIPS: UPDATES TO HEALTHY MARRIAGE AND RELATIONSHIP EDUCATION PROGRAMMINGHHSP233201500064I/HHSP23337001T
45.
2014ASSESSING THE COST AND IMPLEMENTATION OF HIGH QUALITY EARLY CARE AND EDUCATION (ACIHQECE)HHSP23320095642WC-01
46.
2014INTERMEDIATE OUTCOMES OF CAREER PATHWAYS PROGRAMSHHSP233200956WC-01
47.
2014CHILD CARE AND DEVELOPMENT FUND (CCDF) POLICIES DATABASE PROJECTHHSP23320095654WC-01
48.
2014EVALUATION OF DOMESTIC HUMAN TRAFFICKING DEMONSTRATION PROJECTSHHSP23320095651WC-01
49.
2014HOMELESS FAMILIES RESEARCH BRIEFSHHSP23320095624WC-01
50.
2014RESPONDING TO INTIMATE VIOLENCE IN RELATIONSHIP PROGRAMS (RIVIR)HHSP23320095651WC-01
51.
2014UNDERSTANDING THE INTERSECTION BETWEEN TANF AND REFUGEE CASH ASSISTANCE SERVICESHHSP23320095624WC-01
52.
2014IMPROVING CHILDREN?S WELL-BEING: IDENTIFYING MECHANISMS AND TIMING OF FAMILY STRENGTHENING PROGRAMS FOR LOW-INCOME FAMILIES THROUGH DIFFERENTIAL EQUATION MODELING90PD0285-01
53.
2013MOTHER AND INFANT HOME VISITING PROGRAM EVALUATION (MIHOPE)HHSP23337003T-03
54.
2013STUDY OF EMPLOYMENT AND ADVANCEMENT OF RACIAL, ETHNIC AND LINGUISTIC MINORITIES90PH0021-02
55.
2013CHILD CARE AND EARLY EDUCATION POLICY AND RESEARCH ANALYSES (CCEEPRA)HHSP23320095631WC-01
56.
2013EARLY HEAD START-CHILD CARE PARTNERSHIPS STUDYHHSP23320095642WC-01
57.
2013EMPLOYMENT AND TRAINING EVIDENCE REVIEWHHSP23320095642WC-01
58.
2013MATERNAL, INFANT AND EARLY CHILDHOOD HOME VISITING EVALUATION (MIHOPE) IIHHSP23320095644WC-01
59.
2013JOB SEARCH ASSISTANCE EVALUATIONHHSP23320095624WC-01
60.
2013CHILD CARE ADMINISTRATIVE DATA ANALYSIS90YE0148-01
61.
2013HEAD START UNIVERSITY PARTNERSHIPS: DUAL GENERATION APPROACHES90YR0073-01
62.
2013HEAD START UNIVERSITY PARTNERSHIPS: DUAL GENERATION APPROACHES90YR0075-01
63.
2013HUMAN SERVICES RESEARCH PARTNERSHIPS: PUERTO RICO 90YR0072-01
64.
2010Computational Prediction of RNA Viral Genome Structures5S06GM008012-40
65.
2009Computational Prediction of RNA Viral Genome Structures5S06GM008012-39
66.
2008Computational Prediction of RNA Viral Genome Structures5S06GM008012-38
67.
2007Computational Prediction of RNA Viral Genome Structures2S06GM008012-37

Publications icon

  Check NIH Public Access Policy Compliance

Loading
Please wait
1. Munoz S, Guerrero FD, Kellogg A, Heekin AM, Leung MY. Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller''s organ, of the cattle tick, Rhipicephalus australis. PLoS One. 2017; 12(2):e0172326.
2. Guerrero FD, Kellogg A, Ogrey AN, Heekin AM, Barrero R, Bellgard MI, Dowd SE, Leung MY. Prediction of G protein-coupled receptor encoding sequences from the synganglion transcriptome of the cattle tick, Rhipicephalus microplus. Ticks Tick Borne Dis. 2016 07; 7(5):670-677.
3. Zhang B, Yehdego DT, Johnson KL, Leung MY, Taufer M. Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce. BMC Struct Biol. 2013; 13 Suppl 1:S3.
4. Yehdego DT, Zhang B, Kodimala VK, Johnson KL, Taufer M, Leung MY. Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce. IEEE Int Symp Parallel Distrib Process Workshops Phd Forum. 2013 May; 2013:520-529.
5. Cruz-Cano R, Lee ML, Leung MY. Logic minimization and rule extraction for identification of functional sites in molecular sequences. BioData Min. 2012 Aug 16; 5(1):10.
6. Schaubert KL, Price DA, Salkowitz JR, Sewell AK, Sidney J, Asher TE, Blondelle SE, Adams S, Marincola FM, Joseph A, Sette A, Douek DC, Ayyavoo V, Storkus W, Leung MY, Ng HL, Yang OO, Goldstein H, Wilson DB, Kan-Mitchell J. Generation of robust CD8+ T-cell responses against subdominant epitopes in conserved regions of HIV-1 by repertoire mining with mimotopes. Eur J Immunol. 2010 Jul; 40(7):1950-62.
7. Licon A, Taufer M, Leung MY, Johnson KL. A Dynamic Programming Algorithm for Finding the Optimal Segmentation of an RNA Sequence in Secondary Structure Predictions. 2nd Int Conf Bioinform Comput Biol (2010). 2010 Mar; 2010:165-170.
8. Rosskopf JJ, Upton JH, Rodarte L, Romero TA, Leung MY, Taufer M, Johnson KL. A 3'' terminal stem-loop structure in Nodamura virus RNA2 forms an essential cis-acting signal for RNA replication. Virus Res. 2010 Jun; 150(1-2):12-21.
9. Taufer M, Licon A, Araiza R, Mireles D, van Batenburg FH, Gultyaev AP, Leung MY. PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. Nucleic Acids Res. 2009 Jan; 37(Database issue):D127-35.
10. Taufer M, Leung MY, Solorio T, Licon A, Mireles D, Araiza R, Johnson KL. RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology. Parallel Comput. 2008 11 01; 34(11):661-680.
11. Chew DS, Leung MY, Choi KP. AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions. BMC Bioinformatics. 2007 May 21; 8:163.
12. Chew DS, Choi KP, Leung MY. Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses. Nucleic Acids Res. 2005 Sep 01; 33(15):e134.
13. McMullin BT, Leung MY, Shanbhag AS, McNulty D, Mabrey JD, Agrawal CM. Correlating subjective and objective descriptors of ultra high molecular weight wear particles from total joint prostheses. Biomaterials. 2006 Feb; 27(5):752-7.
14. Leung MY, Choi KP, Xia A, Chen LH. Nonrandom clusters of palindromes in herpesvirus genomes. J Comput Biol. 2005 Apr; 12(3):331-54.
15. Chew DS, Choi KP, Heidner H, Leung MY. Palindromes in SARS and Other Coronaviruses. INFORMS J Comput. 2004; 16(4):331-340.
16. Leung MY, Marsh GM, Speed TP. Over- and underrepresentation of short DNA words in herpesvirus genomes. J Comput Biol. 1996; 3(3):345-60.
17. Leung MY, Blaisdell BE, Burge C, Karlin S. An efficient algorithm for identifying matches with errors in multiple long molecular sequences. J Mol Biol. 1991 Oct 20; 221(4):1367-78.
18. Karlin S, Morris M, Ghandour G, Leung MY. Algorithms for identifying local molecular sequence features. Comput Appl Biosci. 1988 Mar; 4(1):41-51.
19. Karlin S, Morris M, Ghandour G, Leung MY. Efficient algorithms for molecular sequence analysis. Proc Natl Acad Sci U S A. 1988 Feb; 85(3):841-5.

Reviews/Chapters/Editorials icon

 

Loading
Please wait
1. Leung MY, Knapka JA, Wagler AE, Rodriguez G, Kirken RA. OncoMiner: A pipeline for bioinformatics analysis of exonic sequence variants in cancer. In: Big Data Analytics in Genomics, Wong KC (editor); Springer, New York, NY. 2016; 373-396.

Research Resources icon

Publications Timeline

Top MeSH Keywords

Tree Map of Keyword Semantic Groups (Categories)

Left-click a node to move down the tree, right-click the graph to move back up the tree

Local representatives can answer questions about the Profiles website or help with editing a profile or issues with profile data. For assistance with this profile:
 
Keyword
Last Name
Institution
 
See all (3) people