Genomics and Big Data - MCBios€¦ · Institute for Genomics, Biocomputing and Biotechnology,...

MCBIOS: XV

15th Annual Meeting

Genomics and Big Data

March 29 – 31, 2018 The Mill Conference Center at MSU

600 Russell St, Starkville, Mississippi

Hosted By: Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University

Hosts and Sponsors

Acknowledgement: This conference is partially supported by a NIGMS (P20 GM103429) grant from NIH and a FDA Scientific Conference Grant from FDA (5R13FD005931-03). Disclaimer: The views presented at this meeting do not necessarily reflect the current or future opinion or policy of the U.S. Food and Drug Administration. Any mention of commercial products is for clarification and not intended as an endorsement.

Table of Contents • MCBIOS organizing committee 1

• MCBIOS board of directors 1

• MCBIOS XV annual meeting program 2

• List of poster presenters 12

• List of oral presenters 20

• MCBIOS 2018 proceedings information 30

• MCBIOS 2019 host and venue 31

• Biographies 32

• MCBIOS App 42

Mid-South Computational Biology and Bioinformatics (MCBIOS)

MCBIOS 2018: XV Annual Conference Organizing Committee

Conference Co-Chairs Bindu Nanduri, Ph.D., MSU, Daniel G. Peterson Ph.D., IGBB/MSU, and Andy Perkins, Ph.D., MSU

Program Co-Chairs Shraddha Thakkar, Ph.D., FDA/NCTR, Prashanti Manda, Ph.D., UNCG and Mary Yang, Ph.D., UALR

• Cesar M. Compadre, Ph.D., Finance Coordinator, Professor, UAMS, Little Rock, AR • Ping Gong, Ph.D., Oral Judging Coordinator, Research Biologist, ERCDC, Vicksburg, MS • George Popescu, Ph.D., Poster Judging Coordinator, Assistant Research Professor, IGBB/MSU

Mississippi State, MS • William S. Sanders, Ph.D., Workshop Coordinator, Manager, IT Research Cyberinfrastructure,

The Jackson Laboratory, Bar Harbor, ME

MCBIOS Board of Directors 2017- 2018

• Bindu Nanduri, Ph.D., President, Board Member through 2020, Associate Professor, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS

• Ramin Homayouni, Ph.D., President-Elect, Board Member through 2021, Professor of Biology, Director of Bioinformatics, University of Memphis, Memphis TN

• Shraddha Thakkar, Ph.D., Past-President, Board Member through 2019, Staff Scientist, FDA National Center for Toxicology Research, Jefferson AR

• Cesar Compadre, Ph.D., Treasurer, Professor, Board Member through 2021, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR

• Inimary Toby, Ph.D., Secretary, Board Member through 2020, Senior Computational Scientist, UT Southwestern Medical Center, Dallas, TX

• Darin E. Jones, Ph.D., Board Member, through 2021 Assistant Professor, University of Arkansas at Little Rock, Little Rock, AR

• Mary Yang, Ph.D., Board Member through 2021 Associate Professor, University of Arkansas at Little Rock, Little Rock, AR

• Ping Gong, Ph.D., Board Member through 2019, Research Biologist, US Army Engineer Research and Development Center, Vicksburg, MS

• Huixiao Hong, Ph.D., Board Member through 2020, Research Chemist, FDA National Center for Toxicology Research, Jefferson, AR

• Yongsheng Bai, Ph.D., Board Member through 2020, Assistant Professor, Indiana State University, Terra Haute, IN

• Wenming Xiao, Ph.D., Board Member through 2021 Principal Investigator, FDA National Center for Toxicology Research, Jefferson, AR

• Prashanti Manda Ph.D., Board Member through 2021, Assistant Professor, University of North Carolina at Greensboro, Greensboro, NC

• Ujwani Nukala, MS, Student Representative, Board Member through 2020, UALR/UAMS joint bioinformatics program, Little Rock, AR

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MCBIOS 2018 XV Annual Meeting Program

Genomics and Big Data Day 1, Thursday March 29rd 2018

11:00am – 05:00pm Registration and Poster Set up “The Gallery, foyer”

01:00pm – 1:20pm Welcome Remarks MCBIOS President - Bindu Nanduri, Ph.D., Associate Professor, Mississippi State University, Mississippi State, MS Opening Remarks Daniel G Peterson, Ph.D., Director, Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS David Shaw, Ph.D., Vice President for Research and Economic Development, Mississippi State University, Mississippi State, MS “The Mississippian Ballroom C”

01:20pm – 02:10pm Keynote Session I Next-Gen Data Science

Russ Wolfinger, Ph.D., Director of Scientific Discovery and Genomics, JMP Life Sciences, SAS Institute, Cary, NC

“The Mississippian Ballroom C” 02:10pm – 02:30pm Break

“foyer” 02:30pm – 03:45pm MCBIOS- JMP Young Scientist Excellence Award Competition for Post-Doctoral

Fellows Session Chair - Ping Gong, Ph.D., US Army Engineer Research & Development Center, Vicksburg, MS “The Mississippian Ballroom C” *Presentations are mentioned in alphabetical order of the last name. The order of presentation will be determined by drawing straws at 2:15 pm. Each presentation will be 15 minutes long including questions

Identification of MiR-486-5p As a Novel Gene Regulator of Liver Detoxification Enzyme Sulfotransferase 2A1 Dongying Li, Ph.D., Post-doctoral Fellow, Post-doctoral Fellow, National Center for Toxicological Research, US FDA, NCTR

Mining pharmacogenomic information from drug labeling using FDALabel database for advancing precision medicine Darshan Mehta, Ph.D., Post-doctoral Fellow, National Center for Toxicological Research, US FDA, NCTR

Protein structure-based virtual screening: Identification of potent natural product-chemotypes as cannabinoid receptor 1 inverse agonists

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Pankaj Pandey, Ph.D., Post-doctoral Fellow University of Mississippi, Oxford, MS Quantitative Target-specific Toxicity Prediction Model (QTTPM): A Novel

Computational Toxicology Approach Integrating Molecular Dynamics Simulation and Machine Learning Sundar Thangapandian, Ph.D., Post-doctoral Fellow University of Illinois Urbana-Champaign, Urbana, IL

SYNTHESIS OF XANTHINE DERVIATIVES FOR THE INHIBITION OF PARG Brian Walker, Ph.D., Post-doctoral Fellow, University of Arkansas at Little Rock, Little Rock, AR

03:45pm – 04:00pm Break “foyer”

04:00pm – 05:15pm MCBIOS- JMP Young Scientist Excellence Award Session for Students Session Chair - Ping Gong, Ph.D., US Army Engineer Research & Development Center, Vicksburg, MS “The Mississippian Ballroom C” *Presentations are mentioned in alphabetical order of the last name. The order of presentation will be determined by drawing straws at 2:15 pm. Each presentation will be 15 minutes long including questions

SIFTING THROUGH BIG DATA: THE SEARCH FOR PERIPHERALLY-RESTRICTED CB1 RECEPTOR ANTAGONISTS AND INVERSE AGONISTS AyoOluwa Aderibigbe, Graduate Student, University of Mississippi, Oxford, MS

SMOTEENNBagging: A novel ensemble resampling and learning approach to QSAR modeling with imbalanced data Gabriel Idakwo, Graduate Student, University of Southern Mississippi, Hattiesburg, MS

Identification of cancer related gene subnetworks based on global optimum searching Dan Li, Graduate Student, University of Arkansas of Little Rock, Little Rock, AR

Altered Neuro-inflammatory Gene Expression in Hippocampus in Major Depressive Disorder Gouri Mahajan, Graduate Student, University of Mississippi Medical Center, Jackson, MS

Transcribed microsatellites as engines of adaptive evolution in common sunflower Chathurani Ranathunge, Graduate Student, Mississippi State University, Starkville, MS

05:15pm – 06:45pm Poster Session (Check the list for detailed poster presenter list) Poster Judging Chair - George Popescu, Ph.D., Mississippi State University, Starkville, MS “The Gallery, foyer” Reception

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“The Gallery, foyer”

Day 2, Friday March 30th 2018 07:30am – 5:00pm Registration

“foyer” 08:00am – 08:50am Keynote Session II

Real World Data and Precision Medicine: Treatment Selection and Dose Optimization Strategies

Lawrence J. Lesko Ph.D., F.C.P., University of Florida, Orlando, FL “The Mississippian Ballroom C”

08:30am-12:00pm Resume Clinic Gladys Awosemo, HRP, Baylor Scott and White health, Texas Meet with an HR professional one-on-one, please sign-up at the time of registration “PINES”

08:50am – 09:15am Break “foyer”

09:15am – 10:35am Breakout Session I, II, III 09:15am – 10:35am Breakout Session I: Plant Omics I

Session Chair – Sorina C. Popescu, Ph.D., Assistant Professor, Mississippi State University, Starkville, MS “RIVERS”

09:15am – 09:35am Session Featured Speaker A pathway-based method to interpret GWAS results Marilyn Warburton, Ph.D., United States Department of Agriculture, Agriculture Research Services, MS

09:35am – 09:50am Marker-assisted-selection coupled with recombinant inbred line genome sequencing identifies a root-knot nematode resistance gene in Upland cotton Martin Wubben, Ph.D., United States Department of Agriculture, Agriculture Research Services, MS

09:50am – 10:05am From Arabidopsis to crops: the QQS orphan gene modulates carbon and nitrogen allocation across species Ling Li, Ph.D., Mississippi State University, Starkville, MS

10:05am - 10:20am Applying multiple transcriptome analyses to understand plant-viroid interactions Ying Wang, Ph.D., Mississippi State University, Starkville, MS

10:20am – 10:35am Analysis of full-length infectious genomic cDNA clones of SPFMV and SPLCV and exploiting the approaches of biotechnology in sweetpotato for virus diseases resistance Kyler Holmes, Graduate Student, Alcorn State University, Lorman, MS

09:15am – 10:35am Breakout Session II: Next generation tools for environment and health research

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Session Chair - Natalia Reyero, Ph.D., US Army Engineer Research and Development Center, Vicksburg MS Student Co-Moderator - Adam Thrash, Graduate Student, Mississippi State University, Starkville, MS “DELTA”

09:15am – 09:35am Session Featured Speaker Next Generation Tools for Environmental Research Natalia Reyero Ph.D., US Army Engineer Research and Development Center, Vicksburg MS

09:35am – 09:50am Keanu: An Interactive Tool for Exploring Sample Content Adam Thrash, Graduate Student, Mississippi State University, Starkville, MS

09:50am – 10:05am Weighted in-network Node Expansion and Ranking (WINNER): a New Approach to Identify Potential Biomarkers Thanh Nguyen, Graduate Student, University of Alabama, Birmingham, AL

10:05am – 10:20am Distinguishing Resistance-Conferring from Susceptible Mutations in Acetohydroxyacid Synthase by High Performance Computing-Enabled Computational Modeling Yan Li, Ph.D., Bennett Aerospace, Cary, NC

10:20am – 10:35am Harnessing a Polyspecific Response to Tumor Associated Carbohydrate Antigens Kori Bohon, Graduate Student, University of Arkansas of Little Rock, Little Rock, AR

09:15am – 10:35am Breakout Session III: Drug Discovery and Precision Medicine Session Chair - Robert J. Doerksen, Ph.D., University of Mississippi, Oxford, MS Student Co-Moderator - Mary Nakamya, Graduate Student, Mississippi State University, Mississippi State, MS “FOOTHILLS”

09:15am – 09:35am Session Featured Speaker Protein structure-based virtual screening: deep learning for precision medicine Robert J. Doerksen, Ph.D., University of Mississippi, Oxford, MS

09:35am – 09:50am “Super Gene Sets”: Toward Integrated Gene-set, Network, and Pathway Analysis Jake Chen, Ph.D., University of Alabama, Birmingham, AL

09:50am – 10:05am Sequencing the BXD family, a cohort for experimental systems genetics and precision medicine David Ashbrook, Ph.D., Post-Doctoral Fellow, University of Tennessee Health Science Center, Memphis, TN

10:05am - 10:20am Development of novel vitamin E analogs as potent radioprotectors Ujwani Nukala, Graduate Student, University of Arkansas at Little Rock, Little Rock, AR

10:20am – 10:35am Assessment release effects of human genome on SNVs calling results from different pipelines based on GIAB data Bohu Pan, Ph.D., Post-Doctoral Fellow, National Center for Toxicological

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Research, US FDA, NCTR 10:35am – 11:00am Break

“foyer” 11:00am – 12:20pm Breakout Session IV, V, VI 11:00am – 12:20pm Breakout Session IV: Plant Omics II

Session Chair – Sorina C. Popescu, Ph.D., Assistant Professor, Mississippi State University, Starkville, MS “RIVERS”

11:00am – 11:20am Session Featured Speaker Focused ion beam-scanning electron microscopy for three-dimensional modelling of cellular ultrastructure Tessa Burch-Smith, Ph.D., University of Tennessee, Knoxville, TN

11:20am – 11:35am Network-centric analysis of pathways for resistance and susceptibility in host pathogen interactions George Popescu, Ph.D., Mississippi State University, Starkville, MS

11:35am – 11:50am The phosphorylated redox proteome of Chlamydomonas reinhardtii: revealing novel means for enzymatic regulation Evan McConnell , Graduate Student, University of North Carolina Chapel Hill, Cary, NC

11:50am – 12:05pm Exploration and Exploitation of Agro-Genomic Variation in Hexaploid Wheat for Yield Stability and End-User Quality Karyn Willyerd, Ph.D., Post-Doctoral Fellow, Oklahoma State University, Stillwater, OK

12:05pm – 12:20pm Transcriptome analysis of abscisic acid-activated protein kinase in abiotic stress in soybean (Glycine max) Saroj Sah, Graduate Student, Mississippi State University, Starkville, MS

11:00am – 12:20pm Breakout Session V: Transcriptomics and Genome Sequencing Session Chair - Brian Counterman, Ph.D., Mississippi State University, Starkville, MS Student Co-Moderator – Didi Ren, Graduate Student, Mississippi State University, Mississippi State, MS “DELTA”

11:00am – 11:20am Session Featured Speaker Patternize: an R package for color pattern variation Brian Counterman, Ph.D., Mississippi State University, Starkville, MS

11:20am – 11:35am Bioinformatic Identification and Phylogenetic Analysis of Putative Chemosensory Receptors in Adult Northern Leopard Frog (Lithobates pipiens) from RNA-Seq Data Ping Gong, Ph.D., US Army Engineer Research & Development Center, Vicksburg, MS

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11:35am – 11:50am An updated newer genome annotation and a evaluation of prior annotation pipeline for the filamentous fungus Cryphonectria parasitica Didi Ren, Graduate Student, Mississippi State University, Starkville, MS

11:50am – 12:05pm Single-cell RNA-seq analysis of retinal ganglion cell subtypes of glaucoma DBA/2J mice Siamak Yousefi, Ph.D., University of Tennessee Health Science Center, Memphis, TN

12:05pm – 12:20pm A Nonparametric Statistical Method for Detection of Serum microRNAs Biomarkers with Complete and Incomplete qPCR Data Wei Zhuang, Ph.D., National Center for Toxicological Research, US FDA, NCTR

11:00am – 12:20pm Breakout Session VI: Big Data and Risk Assessment Session Chair – Minjun Chen, Ph.D., National Center for Toxicological Research, US FDA, NCTR “FOOTHILLS”

11:00am – 11:20am Session Featured Speaker Systems Biology and Big Data: Little Mitochondria as a Big Example William Mattes, Ph.D., National Center for Toxicological Research, US FDA, NCTR

11:20am – 11:35am Chasing the Ghost of Lamisil (terbinafine) Toxicity Grover P Miller, Ph.D., University of Arkansas for Medical Sciences, Little Rock, AR

11:35am – 11:50am Infer the in vivo Point of Departure with ToxCast in vitro Assay Data Using a Robust Learning Approach Dong Wang, Ph.D., National Center for Toxicological Research, US FDA, NCTR

11:50am – 12:05pm Develop predictive model for assessing drug-induced liver injury in humans Minjun Chen, Ph.D., National Center for Toxicological Research, US FDA, NCTR

12:05pm – 12:20pm Enzyme kinetics and toxicological evaluation of diallyl sulfide analogs for their novel role as CYP2E1 inhibitors using molecular modeling and in vitro methods Arif Rahman, Graduate Student, University of Tennessee Health Science Center, Memphis, TN

12:20pm – 01:30pm Lunch and MCBIOS Business Meeting MCBIOS Treasurer Report Cesar M. Compadre, Ph.D., MCBIOS Treasurer, University of Arkansas for Medical Sciences, Little Rock, AR MCBIOS Updates and Election of Officers Shraddha Thakkar, Ph.D., MCBIOS Past President, National Center for Toxicological Research, US FDA, NCTR Candidates running for election (Term 2018 – 2022): President Elect: Weida Tong, Ph.D., National Center for Toxicological Research, US FDA, NCTR Board Members: Robert J. Doerksen, Ph.D., University of Mississippi, Oxford, MS Jake Chen, Ph.D., University of Alabama, Birmingham, AL “The Mississippian Ballroom A and B”

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01:30pm - 06:00pm Resume Clinic Gladys Awosemo, HRP, Baylor Scott and White health, Texas Meet with an HR professional one-on-one, please sign-up at the time of registration “PINES”

01:30pm – 03:15pm Workshop I and II 01:30pm – 03:15pm Workshop I

Advanced Data Analytics using Jmp Genomics Wenjun Bao, Ph.D., JMP Life Sciences, SAS Institute, Cary, NC

“FOOTHILLS” 01:30pm – 03:15pm Workshop II

Career Development Workshop for Young Scientist Inimary Toby, Ph.D., University of Texas Southwestern, Dallas, TX

“DELTA” 03:15pm – 03:50pm Keynote Session III

No-Boundary Thinking: Defining Problems So Their Solutions Matter Steve Jennings, Ph.D., University of Arkansas at Little Rock, Little Rock, AR “The Mississippian Ballroom C”

03:50pm – 04:00pm Break “foyer”

04:00pm – 05:45pm Workshop III and IV 04:00pm – 05:45pm Workshop III

MCBIOS and No-Boundary Thinking Joint Bioinformatics Research workshop Session chair - Steve Jennings, Ph.D., University of Arkansas at Little Rock, Little Rock, AR Presentations:

• Encoding biomedical knowledge using hetnets Daniel Himmelstein, Ph.D., University of Pennsylvania, Philadelphia, PN

• Microbial interactions and microbe-host interactions Hongmei Jiang Ph.D., Northwestern University, Evanston, IL

• Evolution as a metaphor for No Boundary Thinking Scott M. Williams, Ph.D., Case Western Reserve University, Cleveland, Ohio

Panel Discussion: Joan Peckham, Ph.D., Professor, University of Rhode Island Xiuzhen Huang, Ph.D., Professor, Arkansas State University Scott M. Williams, Ph.D., Professor, Case Western Reserve University Hongmei Jiang, Ph.D., Associate Professor, Northwestern University Daniel Himmelstein, Ph.D., Postdoctoral Fellow, University of Pennsylvania Best Question Awards: “DELTA”

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04:00pm – 05:45pm Workshop IV Next-Generation Sequencing analysis using Galaxy

Binsheng Gong, Ph.D., National Center for Toxicological Research, US FDA, NCTR “FOOTHILLS”

Day 3, Saturday, March 31th, 2018 07:00am – 08:30am Board Meeting (new and old board) and Breakfast

“Courtyard Marriott meeting room” 09:00am – 09:50am Keynote Session IV

Informatics Tools for Big Biologicals and Small Drug Molecules William J Welsh, Ph.D., Norman H. Edelman Professor in Bioinformatics,

Rutgers University, New Brunswick, NJ “The Mississippian Ballroom C”


10:00am – 11:20am Breakout Session VII, VIII, IX 10:00am – 11:20am Breakout Session VII: Genomics and Proteomics application

Session Chair - Zhichao Liu, Ph.D., National Center for Toxicological Research, US FDA, NCTR “RIVERS”

10:00am – 10:20am Session Featured Speaker Complete genome sequence of Pythium brassicum P1, an oomycete root pathogen: insights into its host specificity to brassicaceae Rakesh Kaundal, Ph.D., Utah State University, Logan, UT

10:20am – 10:35am Two-level Deep Convolutional Neural Networks Applied to Protein Contact Prediction Badri Adhikari, Ph.D., University of Missouri, St. Louis, MO

10:35am – 10:50am PROTEOMIC ANALYSIS OF ERYTHROCYTE STORAGE LESIONS IN UNITS OF STORED CANINE PACKED RED BLOOD CELLS John Thomason, Ph.D., Mississippi State University, Starkville, MS

10:50am – 11:05am Benchmarking Protein Residue-Residue Contact Prediction Using Random Forests and Deep Networks Joseph Luttrell IV, Graduate Student, University of Southern Mississippi, Hattiesburg, MS

11:05am – 11:20am WIPER: Weighted in-path edge ranking for biomolecular association networks Zongliang Yue, Graduate Student, University of Alabama, Birmingham, AL

10:00am – 11:20am Breakout Session VIII – Genomics and Infectious Disease Session Chair – Stephen Pruett, Ph.D., Mississippi State University, Starkville, MS Student Co-Moderator - Gizem Dimlioglu, Graduate Student, Mississippi State University, Mississippi State, MS “DELTA”

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10:00am – 10:20am Session Featured Speaker Machine Learning Analysis of the Relationship between Changes in Immunological Parameters and Changes in Resistance to Listeria Monocytogenes: A New Approach for Risk Assessment and Systems Immunology Stephen Pruett, Ph.D., Mississippi State University, Starkville, MS

10:20am – 10:35am Effects of Ethanol on Escherichia coli-mediated sepsis: Differences Between Changes in Gene Expression Early and Late in the Course of Infection. Wei Tan, Ph.D., Mississippi State University, Starkville, MS

10:35am – 10:50am Characterization of the Gut Microbiome of channel catfish following florfenicol treatment Hossam Abdelhamed, Ph.D., Mississippi State University, Starkville, MS

10:50am – 11:05am Identification of host genes determining the pathogenesis of influenza A viruses in mice using machine learning Hamilton Wan, The Mississippi School for Mathematics and Science, Starkville, MS

11:05am – 11:20am Prediction of Chronic Diseases on Imbalanced Data with Deep Neural Networks Andrew Maxwell, Graduate Student, University of Southern Mississippi, Hattiesburg, MS

10:00am – 11:15am Breakout Session IX - MCBIOS Group Projects Session Co-Chairs – Shraddha Thakkar, Ph.D., National Center for Toxicological Research, US FDA, NCTR William Sanders, Ph.D., IT Research Cyberinfrastructure, The Jackson Laboratory, Bar Harbor, ME “FOOTHILLS”

10:00am – 10:25am Sensitivity and reproducibility of onco-panel sequencing across multiple laboratories and technologies: An SEQC2 Component Study Joshua Xu, Ph.D., National Center for Toxicological Research, US FDA, NCTR

10:25am – 10:50am Predicting Drug-Induced Liver Injury (DILI) – Comparing in silico, genomic and Tox21 screening methods Shraddha Thakkar, Ph.D., National Center for Toxicological Research, US FDA, NCTR

10:50am – 11:15am MCBIOS Timber Rattlesnake Genome Project: Current Status and Lessons Learned William Sanders, Ph.D., IT Research Cyberinfrastructure, The Jackson Laboratory, Bar Harbor, ME


11:30am –12:20pm Keynote Session V A decade of MAQC effort and its contribution to our understanding of

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high-throughput genomics technologies Weida Tong, Ph.D., Director, Division of Bioinformatics and Biostatistics,

National Center for Toxicological Research, US FDA, NCTR “The Mississippian Ballroom C”

12:20pm – 01:30pm Lunch MCBIOS New leadership - Shraddha Thakkar, Ph.D., National Center for Toxicological Research, US FDA, NCTR MCBIOS 2018-19 President - Ramin Homayouni, Ph.D., University of Memphis, TN MCBIOS 2019 XVI Annual Meeting - Jake Chen, Ph.D., University of Alabama, Birmingham, AL Closing Remarks – William Slikker Jr., Ph.D., National Center for Toxicological Research, US FDA, NCTR Awards MCBIOS Best Poster Award - George Popescu, Ph.D., Mississippi State University, Starkville, MS MCBIOS-JMP Young Scientist Excellence Award - Ping Gong, Ph.D., US Army Engineer Research & Development Center, Vicksburg, MS MCBIOS Service Award - Bindu Nanduri, Ph.D., Associate Professor, Mississippi State University, Mississippi State, MS “The Mississippian Ballrooms A and B”

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List of Poster Presenters Poster No

Name Affiliation Membership type

Title of poster presentation

1 Adam Thrash Mississippi State University, Starkville, MS

Student Quack: A Tool for Rapid FASTQ Quality Assurance

2 Adam Thrash Mississippi State University, Starkville, MS

Student A Machine Learning Approach to Genome Assessment

3 Adef Kordon Mississippi State University, Starkville, MS

Student Phagocytic and Bactericidal Properties of B cells in Channel Catfish Exposed to Edwardsiella ictaluri Live Attenuated Vaccine and Wild-Type Strains

4 Afzaal Mohammed

Mississippi State University, Starkville, MS

Student Protein Expression in Adolescent Rats Exposed to ∆9-Tetrahydrocannabinol During Juvenile Ages

5 Aleksandra Perz Oklahoma Medical Research Foundation, Oklahoma City, OK

Student MNEMONIC – METAGENOMIC EXPERIMENT MINING TO CREATE AN OTU NETWORK OF INHABITANT CORRELATIONS

6 Alexander Lim Oklahoma State University, Stillwater, OK

Student Data-Driven Genomic Surveillance of Microbial Drug Resistance Using Oxford Nanopore Single Molecule Sequencing Technology

7 Allen Shack Mississippi State University, Starkville, MS

Professional IMPACT OF IMPAIRED POLYAMINE TRANSPORT ON STREPTOCOCCUS PNEUMONIAE

8 Andrew Stiemke University of Tennessee Health Science Center, Memphis, TN

Student Systems Genetics of Optic Nerve Axon Death

9 Brian Delavan University of Arkansas at Little Rock, Little Rock, AR

Student Comprehensive Evaluation of Stability and Reproducibility for Deep Learning Algorithms in Cancer Prognosis Prediction

10 Bryan Naidenov Oklahoma State University, Stillwater, OK

Student Exposing the hidden chromatin regulatory framework with recurrent deep learning and genomic sequence data

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11 Caleb Benson Mississippi State University, Starkville, MS

Student Transposable Element activity and the origin of novel butterfly wing patterns

12 Callie Whitfield Mississippi State University, Starkville, MS

Student Illumina Maize Genome Sequencing Data Analysis for Identification of Fungal Resistance Genes in Maize

13 Caroline Melton University of Memphis, Memphis, TN

Student A METHOD FOR HAPLOTYING POLYPLOID ORGANELLAR GENOMES

14 Chaoyang Zhang University of Southern Mississippi, Hattiesburg, MS

Professional CECOND: A Novel CUCKOO Filter-Based Error Correction Method for Next Generation Sequencing Data

15 Chase Brown University of Oklahoma Health Sciences Center, Oklahoma City, OK

Student Metadata Extraction Neural Architectures for Large Scale Signature Extraction

16 Cord Carter University of Arkansas for Medical Sciences, Little Rock, AR

Student Development of an Annotated discriptors that can be used to Analyze and Predict Idiosyncratic Liver Injury

17 Courtney Hunter Mississippi State University, Starkville, MS

Student RNA Sequencing Reveals HCN4 as a New Mediator of Airway Hyper-responsiveness in a Spontaneous, Naturally Occurring Equine Asthma Model

18 Cristian Loaiza Utah State University, Logan, UT

Student Plant-mSubP: a computational framework for the prediction of single and multi-target protein subcellular localization using integrated machine-learning approaches

19 Dafne Alves Oliveira


Student In-Silico Analysis of Cis- Regulatory Elements of Candidate Genes Related to Reduced Aflatoxin Accumulation in Maize.

20 Daniel Acheampong

University of Arkansas at Little Rock, Little Rock, AR

Student Genome-wide DNA methylation analysis reveals aberrant epigenetic age and glucocorticoid related genes in blood of breast cancer patients

21 David Mery University of Arkansas for Medical

Student The Sesquiterpene Lactone Parthenin, from Parthenium hysteropherus, Ablates Acute Myelogenous Leukemia (AML)

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Sciences, Little Rock, AR

23 Diem Trang Pham University of Memphis, Memphis, TN

Student General-purpose Toolkit for Discovery and Visualization of Heteroplasmy in Cytoplasmic Genomes

24 Doga Demirel University of Central Arkansas, Conway, AR

Student Partition-based Optimization Model for Generative Anatomy Modeling Language (POM-GAML) for Anatomy Modeling

25 Dustyn Barnette University of Arkansas for Medical Sciences, Little Rock, AR

Student Terbinafine bioactivation: Determining preferred pathway to a reactive metabolite using predictive and experimental approaches

27 Eda Ozdemir Mississippi State University, Starkville, MS

Student Development and Visualization of Bioluminescent Virulence A. hydrophila in Live Catfish

28 Emine Bircan University of Arkansas for Medical Sciences, Little Rock, AR

Student Integration of Tracts of Homozygosity Regions and region-specific nucleotide repeat reveal expanded CpG island of CDKN2C in Lung Cancer

29 Fang Chen Jackson State University, Jackson, MS

Student Analyzing Spaceflight Omics Data: Identifying Radiation Exposure Biomarkers from Mouse Blood Transcriptome

30 Felicia Parish Mississippi State University, Starkville, MS

Student Molecular Signaling Pathways Associated with Aflatoxin Reduction in Corn

31 Gizem Dimlioglu Mississippi State University, Starkville, MS

Student Determining the function of ILKs (Integrin-Linked Kinases) in Innate Immunity and Hyperosmotic Stress Response

32 Gokhan Yavas National Center for Toxicological Research, US FDA, NCTR

Professional CQAT: Contig Quality Assessment Tool

33 Hamilton Wan The Mississippi School for Mathematics and Science, Starkville, MS

High School The Effects of Vaccination on the Spread of Ebola

34 Hasan Tekedar Mississippi State

Professional Post-Doc

Comparative Mobilome Analysis of Aeromonas hydrophila Strains

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University, Starkville, MS

35 Hunter Porter University of Oklahoma Health Sciences Center, Oklahoma City, OK

Student Testing the Limits of the Epigenetic Clock

36 James Jackson Mississippi State University, Starkville, MS

Student Pneumococcal Resistance to Granule-mediated Killing by Neutrophils

37 Jared Cole Mississippi State University, Starkville, MS

Student Demographic Modeling Utilizing the Joint Allele Frequency Spectrum in two hybridizing Heliconius species

38 Jeremy Winders Mississippi State University, Starkville, MS

Student Discovery of Antifungal Metabolites in Maize Cob Tissue

39 Jing Jin University of Arkansas for Medical Sciences, Little Rock, AR

Student Tracts of Homozygosity and Linkage Disequilibrium Profiles in Lung Cancer

40 Joseph Noonan Mississippi State University, Starkville, MS

Student IDENTIFICATION OF MAIZE ANTIMICROBIAL PEPTIDE GENES BASED ON HOMOLOGY DATA-MINING FROM COMPREHENSIVE DATABASES

41 Kurt Gust Engineer Research and Development Center, Vicksburg, MS

Professional Similar to the Insensitive Munition (IM) nitroguanidine, the IM 1-methyl-3-nitroguanidine Also Exhibits Enhanced Toxicity when UV-Degraded

42 LEI LI Mississippi State University, Starkville, MS


Identifying potential agents causing fish disease outbreaks in Mississippi Delta Using Metagenomics

43 Leihong Wu National Center for Toxicological Research, US FDA, NCTR

Professional Deep learning for food contamination detection

44 Liangqun Lu University of Memphis, Memphis, TN

Student Clinical Subgroup-Specific PTSD Classification and Biomarker Identification

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45 Lindsey Burcham Mississippi State University, Starkville, MS

Student Uncharacterized operon of Streptococcus pneumoniae alters cellular metabolism and oxidative stress response during zinc-starvation

46 Lizhong Ding Indiana State University, Terre Haute, IN

Student Quantification of expressional correlation coefficient changes of miRNA and mRNA for TCGA next generation sequencing data using traditional hierarchical clustering

47 Luis Rodriguez Caro


Student Genetics of sexually dimorphic wing pattern development in the Dogface Butterfly

48 Mary Davis University of Arkansas for Medical Sciences, Little Rock, AR

Student CYP2C19 and 3A4 Generate a Potentially Toxic, Reactive Terbinafine Metabolite as Revealed through Modeling and Experimental Methods

49 Mary Francis Nakamya


Student Effect of the impaired cadaverine biosynthesis gene (∆cadA) on Streptococcus pneumoniae TIGR4 transcriptome

50 MD ABUL HAYAT University of Arkansas, Fayetteville, AR

Student Predicting Dehydration in Pediatric Patients with Peripheral Venous Waveforms

52 Md Imran Sarker Jackson State University, Jackson, MS

Student A COMPARATIVE PHYLOGENETIC EVALUATIONOF CHLOROPLAST IT’S SEQUENCES TO ANALYZE THE BIOACTIVITY IN MEDICINAL PLANTS: ACASE STUDY OF CLERODENDRUM PALNT GENUS (LAMIACEAE)

53 Moses Ayoola Mississippi State University, Starkville, MS

Student IMPACT OF IMPAIRED POLYAMINE BIOSYNTHESIS ON STREPTOCOCCUS PNEUMONIAE TIGR4 GENE EXPRESSION

54 Mustafa Muhammad


Student The Effect of Oryzalin on Secondary Roots of Wild Type, ILK 1, ILK 4, and ILK 5 Genes

55 Najmeh Setareh Nejat


Student An analysis of pathogen susceptibility pathways in Solanum lycopersicum

56 Nan Wang New Jersey City University, Jersey City, NJ

Professional miRDisc: A Novel Computational Program for microRNA Discovery from Short Deep Sequencing Reads and Transcriptomic Assembly

57 Navatha Alugubelly

Mississippi State

Student Changes of Protein Expression Profiles in the Amygdala of Adolescent Rats Exposed

Page 16 of 44

University, Starkville, MS

Developmentally to Chlorpyrifos

58 Nikhil Nuthalapati Mississippi State University, Starkville, MS

Student Transcriptomic analysis of early B-cell development in the chicken embryo

59 Norbert Bokros Mississippi State University, Starkville, MS

Student The Examination of MAP3Ks in Plants and Protein Kinase Characterization

60 Oluwaseun Ogunola


Student CREATION AND MAPPING OF A NEW POPULATION TO IDENTIFY NOVEL QTLS FOR AFLATOXIN ACCUMULATION RESISTANCE IN MAIZE

61 Oluwatobi quadri University of Texas Southwestern, Dallas, TX

Student Computational approaches for characterization of Novel Antigens in Malaria

62 Philip Berg Mississippi State University, Starkville, MS

Student The dynamics of reversible Cys-oxidized proteome in plant immunity

63 Pulin Agrawal University of Memphis, Memphis, TN

Student Characterization and Classification of Gene Expression Data with Sparse Autoencoders

64 QUANG TRAN University of Memphis, Memphis, TN

Student 3M: Min Max Hashing for Classification of Short Reads in Metagenomic Applications

65 Rachel Royston Mississippi State University, Starkville, MS

Student Identification and Isolation of Resistance Genes from Mp715 (Zea mays)

66 Recep Erol University of Central Arkansas, Conway, AR

Student Cloud-Based Transfer Learning for Skin Cancer Monitoring and Diagnosis

67 Sujoy Roy University of Memphis, Memphis, TN

Professional Post Doc

Literature Informed Bayesian Sparse Generalized Linear Modeling for Class Prediction

68 Robin Ghosh Jackson State University, Jackson, MS

Student EXPLORING COMPLEX DISEASE PROTEIN RELATIONSHIPS IN ALZHEIMER'S DISEASE USING PROTEIN INTERACTOME AND COMPUTATIONAL GENE SILENCING

69 Russell Carr Mississippi State University,

Professional Alteration of Endocannabinoid Signaling during Juvenile Exposure to Chlorpyrifos Plays a Role in the Persistent Changes in Gene Expression in

Page 17 of 44

Starkville, MS Adolescent Rats.

70 Salih Kumru Mississippi State University, Starkville, MS

Student Genome Sequence and Comparative Genomics of Fish Pathogen Aeromonas bestiarum GA97-22

71 Samuel Kakraba University of Arkansas at Little Rock, Little Rock, AR

Student using quantitative structure-activity relationships in drug discovery to identify potential drugs to treat neurodegenerative diseases

72 Sarbagya Shakya University of Southern Mississippi, Hattiesburg, MS

Student Video-based Human Action and Activity Recognition for Elderly Health Care Application

74 Skylar Connor University of Arkansas at Little Rock, Little Rock, AR

Student Ribosomal Proteins for Better Resolution in Microbial Taxonomy

75 Sujoy Roy University of Memphis, Memphis, TN

Professional Post Doc

Evaluation of Gene Co-Expression Networks Using Literature Derived Functional Cohesion

76 Tanmay Bera National Center for Toxicological Research, US FDA, NCTR


Towards automated identification of food contaminating beetle species: methods to improve imaging and image analysis

77 Ted Ling Hu University of Memphis, Memphis, TN

Student DATA-DRIVEN FEATURE SELECTION FOR TRANSCRIPTOMICS DATA USING SINGULAR VALUE DECOMPOSITION

78 Thomas Hahn University of Arkansas at Little Rock, Little Rock, AR

Student Uncovering Imperatively Hidden Objects (IHO) to complete feature selection in order to enhance accuracy and predictive power of supervised Machine Learning (ML) algorithms

79 Thualfeqar Almohanna


Student Optimization of Protein Identification for Label-Free Quantitative Proteomics (LC-MS/MS) of Sweet Potato

80 Tianjiao Shen University of Arkansas for Medical Sciences, Little Rock, AR

Student Integrative Genomic Analysis of MARCO, EPAS1, SFTPB, KCNK3, ACADL with Lung Cancer

81 Ting Li University of Arkansas at Little Rock,

Student Voxel-Based Morphometry Study of Alzheimer’s Disease

Page 18 of 44

Little Rock, AR

82 Victoria Jefferson Mississippi State University, Starkville, MS

Student Proteogenomic mapping reveals previously unannotated coding region in Bovine Herpesvirus 1 genome

83 Vincent Langat Jackson State University, Jackson, MS

Student USING MOLECULAR MODELING TO ESTABLISH CONNECTION BETWEEN PARKINSON'S DISEASE AND PESTICIDES

84 Visanu Wanchai University of Arkansas for Medical Sciences, Little Rock, AR

Student Analyses of genome quality scores across 120,000 genomes

85 Visanu Wanchai University of Arkansas for Medical Sciences, Little Rock, AR

Student Identifying repetitive elements associated BE/EAC-related traits using exome sequencing data

86 Winston Miller University of Memphis, Memphis, TN

Student Extended Automated Analysis Package using System on a Chip (E-ABAPSoC)

88 Xiavan Roopnarinesingh

University of Oklahoma Health Sciences Center, Oklahoma City, OK

Student Gene Function Prediction Using Global Meta-Analysis of Promoter-Associated CpG Comethylation

89 Xinqing Dai Indiana State University, Terre Haute, IN

Student Hierarchical clustering of hypergraphs using microRNA and mRNA expression data from TCGA

90 Zheyun Feng Indiana State University, Terre Haute, IN

Student Detection of clusters of miRNA and mRNA based on their quantified changes of expressional correlation coefficients from TCGA data using maximum weighted merger method (MWMM)

91 Zhichao Liu National Center for Toxicological Research, US FDA, NCTR

Professional Performance Comparison and Scaling Bioinformatics Applications

92 Zhongning Chen University of Arkansas for Medical Sciences, Little Rock, AR

Student Exploring the non-small-cell lung cancer (NSCLC) clinical stage progression via miRNA and mRNA expression and interaction patterns.

Page 19 of 44

List of Oral Presenters No Name Affiliation Membership

Type Title Session

Determination

Time Date Location

1 Adam Thrash


Student Keanu: An Interactive Tool for Exploring Sample Content

Session - 2: Next generation tools for environment and health research

9:35-9:50AM

3/30/2018 DELTA

2 Andrew Maxwell

University of Southern Mississippi, Hattiesburg, MS

Student Prediction of Chronic Diseases on Imbalanced Data with Deep Neural Networks

Session – 8: Genomics and Infectious Disease

11:05-11:20AM

3/31/2018 DELTA

3 Arif Rahman

University of Tennessee Health Science Center, Memphis, TN

Student Enzyme kinetics and toxicological evaluation of diallyl sulfide analogs for their novel role as CYP2E1 inhibitors using molecular modeling and in vitro methods

Session - 6: Big Data and Risk Assessment

12:05-12:20PM

3/30/2018 FOOTHILLS

4 AyoOluwa Aderibigbe

University of Mississippi, Oxford, MS

Student SIFTING THROUGH BIG DATA: THE SEARCH FOR PERIPHERALLY-RESTRICTED CB1 RECEPTOR ANTAGONISTS AND INVERSE AGONISTS

MCBIOS-JMP Young Scientist Award

04:00 – 05:15pm

3/29/2018 The Mississippian Ballroom C

5 Badri Adhikari

University of Missouri, St. Louis

Professional Two-level Deep Convolutional Neural Networks Applied to Protein Contact Prediction

Session - 7: Genomics and Proteomics application

10:20-10:35AM

3/31/2018 RIVERS

6 Binsheng Gong

National Center for Toxicological Research, US FDA, NCTR

Professional Next-Generation Sequencing using Galaxy

Workshop - 4: Next-Generation Sequencing using Galaxy

4:00-5:45PM

3/30/2018 FOOTHILLS

7 Bohu Pan National Center for Toxicological


Assessment release effects of human genome

Session - 3: Drug Discovery

10:20-10:35AM

3/30/2018 FOOTHILLS

Page 20 of 44

Research, US FDA, NCTR

on SNVs calling results from different pipelines based on GIAB data

and Precision Medicine

8 Brian Counterman


Professional Patternize: an R package for color pattern variation

Session - 5: Transcriptomics and Genome Sequencing

11:00-11:20AM

3/30/2018 DELTA

9 Brian Walker



SYNTHESIS OF XANTHINE DERVIATIVES FOR THE INHIBITION OF PARG


02:30 – 03:45pm


10 Chathurani Ranathunge


Student Transcribed microsatellites as engines of adaptive evolution in common sunflower


04:00 – 05:15pm


11 Dan Li University of Arkansas at Little Rock, Little Rock, AR

Student Identification of cancer related gene subnetworks based on global optimum searching


04:00 – 05:15pm


12 Daniel Himmelstein

University of Pennsylvania, Philadelphia, PN


Encoding biomedical knowledge using hetnets

Workshop - 3: No-Boundry Thinking Bioinformatics Research workshop

4:00-5:45PM

3/30/2018 DELTA

13 Darshan Mehta



Mining pharmacogenomic information from drug labeling using FDALabel database for advancing precision medicine


02:30 – 03:45pm


14 David Ashbrook

University of Tennessee Health Science Center, Memphis,


Sequencing the BXD family, a cohort for experimental systems genetics and precision

Session - 3: Drug Discovery and Precision Medicine

9:50-10:05AM

3/30/2018 FOOTHILLS

Page 21 of 44

TN medicine

15 Dong Wang National Center for Toxicological Research, US FDA, NCTR

Professional Infer the in vivo Point of Departure with ToxCast in vitro Assay Data Using a Robust Learning Approach


11:35-11:50AM

3/30/2018 FOOTHILLS

16 Dongying Li National Center for Toxicological Research, US FDA, NCTR


Identification of MiR-486-5p As A Novel Gene Regulator of Liver Detoxification Enzyme Sulfotransferase 2A1


02:30 – 03:45pm


17 Evan McConnell

University of North Carolina Chapel Hill, Cary, NC

Student The phosphorylated redox proteome of Chlamydomonas reinhardtii: revealing novel means for enzymatic regulation.

Session -4: Plant Omics II

11:35-11:50AM

3/30/2018 RIVERS

18 Gabriel Idakwo


Student SMOTEENNBagging: A novel ensemble resampling and learning approach to QSAR modeling with imbalanced data


04:00 – 05:15pm


19 George Popescu


Professional Network-centric analysis of pathways for resistance and susceptibility in host pathogen interactions


11:20-11:35AM

3/30/2018 RIVERS

20 Gouri Mahajan

University of Mississippi Medical Center, Jackson, MS

Student Altered Neuro-inflammatory Gene Expression in Hippocampus in Major Depressive Disorder


04:00 – 05:15pm


21 Grover P Miller

University of Arkansas for Medical Sciences,

Professional Chasing the Ghost of Lamisil (terbinafine) Toxicit


11:20-11:35AM

3/30/2018 FOOTHILLS

Page 22 of 44

Little Rock, AR

22 Hamilton Wan

The Mississippi School for Mathematics and Science, Starkville, MS

High School Identification of host genes determining the pathogenesis of influenza A viruses in mice using machine learning


10:50-11:05AM

3/31/2018 DELTA

23 Hongmei Jiang

Northwestern University, Evanston, IL

Professional Microbial interactions and microbe-host interactions

Workshop - 3: No-Boundry Thinking Bioinformatics Research workshop

4:00-5:45PM

3/30/2018 DELTA

24 Hossam Abdelhamed


Professional Characterization of the Gut Microbiome of channel catfish following florfenicol treatment


10:35-10:50AM

3/31/2018 DELTA

25 Inimary Toby

University of Texas Southwestern, Dallas, TX

Professional Carrer Development Workshop for Young Scientist

Workshop - 2: Carrer Development Workshop for Young Scientist

1:30-3:15PM

3/30/2018 DELTA

26 Jake Chen University of Alabama, Birmingham, AL

Professional “Super Gene Sets”: Toward Integrated Gene-set, Network, and Pathway Analysis


9:35-9:50AM

3/30/2018 FOOTHILLS

27 John Thomason


Professional PROTEOMIC ANALYSIS OF ERYTHROCYTE STORAGE LESIONS IN UNITS OF STORED CANINE PACKED RED BLOOD CELLS


10:35-10:50AM

3/31/2018 RIVERS

28 Joseph Luttrell IV


Student Benchmarking Protein Residue-Residue Contact Prediction Using Random Forests and Deep Networks


10:50-11:05AM

3/31/2018 RIVERS

29 Joshua Xu National Professional Sensitivity and Session - 9: 10:00- 3/31/2018 FOOTH

Page 23 of 44

Center for Toxicological Research, US FDA, NCTR

reproducibility of onco-panel sequencing across multiple laboratories and technologies: An SEQC2 Component Study

MCBIOS Group Projects

10:25AM

ILLS

30 Karyn Willyerd

Oklahoma State University, Stillwater, OK


Exploration and Exploitation of Agro-Genomic Variation in Hexaploid Wheat for Yield Stability and End-User Quality


11:50AM-12:05PM

3/30/2018 RIVERS

31 Kori Bohon University of Arkansas at Little Rock, Little Rock, AR

Student Harnessing a Polyspecific Response to Tumor Associated Carbohydrate Antigens


10:20-10:35AM

3/30/2018 DELTA

32 Kyler Holmes

Alcorn State University, Lorman, MS

Student Analysis of full-length infectious genomic cDNA clones of SPFMV and SPLCV and exploiting the approaches of biotechnology in sweetpotato for virus diseases resistance

Session - 1: Plant Omics I

10:20-10:35AM

3/30/2018 RIVERS

33 Lawrance J. Lesko

University of Florida, Orlando, FL

Professional Real World Data and Precision Medicine: Treatment Selection and Dose Optimization Strategies

Keynote Speaker

8:00-8:50AM


34 Ling Li Mississippi State University, Starkville, MS

Professional From Arabidopsis to crops: the QQS orphan gene modulates carbon and nitrogen allocation across species


9:50-10:05AM

3/30/2018 RIVERS

35 Marilyn Warburton

United States Department

Professional A pathway-based method to interpret GWAS


9:15-9:35AM

3/30/2018 RIVERS

Page 24 of 44

of Agriculture, Agriculture Research Services, MS

results

36 Martin Wubben

United States Department of Agriculture, Agriculture Research Services, MS

Professional Marker-assisted-selection coupled with recombinant inbred line genome sequencing identifies a root-knot nematode resistance gene in Upland cotton


9:35-9:50AM

3/30/2018 RIVERS

37 Minjun Chen


Professional Develop predictive model for assessing drug-induced liver injury in humans


11:50AM-12:05PM

3/30/2018 FOOTHILLS

38 Natalia Reyero


Professional Tools for environmental and predictive biology


9:15-9:35AM

3/30/2018 DELTA

39 Pankaj Pandey



Protein structure-based virtual screening: Identification of potent natural product-chemotypes as cannabinoid receptor 1 inverse agonists


02:30 – 03:45pm


40 Ping Gong US Army Engineer Research & Development Center, Vicksburg, MS

Professional Bioinformatic Identification and Phylogenetic Analysis of Putative Chemosensory Receptors in Adult Northern Leopard Frog (Lithobates pipiens) from RNA-Seq Data


11:20-11:35AM

3/30/2018 DELTA

41 Rakesh Kaundal

Utah State University,

Professional Complete genome

Session - 7: Genomics

10:00-10:20

3/31/2018 RIVERS

Page 25 of 44

Logan, UT sequence of Pythium brassicum P1, an oomycete root pathogen: insights into its host specificity to brassicaceae

and Proteomics application

AM

42 Robert J. Doerksen


Professional Protein structure-based virtual screening: deep learning for presision medicine


9:15-9:35AM

3/30/2018 FOOTHILLS

43 Russ Wolfinger

JMP Life Sciences, SAS Institute, Cary, NC

Professional Next-Gen Data Science

Keynote Speaker

1:20-2:10PM


44 Saroj Sah Mississippi State University, Starkville, MS

Student Transcriptome analysis of abscisic acid-activated protein kinase in abiotic stress in soybean (Glycine max)


12:05-12:20PM

3/30/2018 RIVERS

45 Scott M. Williams

Case Western Reserve University, Cleveland, Ohio

Professional Evolution as a metaphor for No Boundary Thinking

Workshop - 3 : No-Boundry Thinking Bioinformatics Research workshop

4:00-5:45PM

3/30/2018 DELTA

46 Shraddha Thakkar


Professional Predicting Drug-Induced Liver Injury (DILI) – Comparing in silico, genomic and Tox21 screening methods

Session - 9: MCBIOS Group Projects

10:25-10:50AM

3/31/2018 FOOTHILLS

47 Siamak Yousefi

University of Tennessee Health Science Center, Memphis, TN

Professional Single-cell RNA-seq analysis of retinal ganglion cell subtypes of glaucoma DBA/2J mice


11:50AM-12:05PM

3/30/2018 DELTA

48 Stephen Pruett

Mississippi State University, Starkville,

Professional Machine Learning Analysis of the Relationship

between Changes

Session – 8: Genomics and Infectious

10:00-10:20AM

3/31/2018 DELTA

Page 26 of 44

MS in Immunological Parameters and

Changes in Resistance to

Listeria Monocytogenes: A New Approach

for Risk Assessment and

Systems Immunology

Disease

49 Steve Jennings


Professional No-Boundary Thinking: Defining Problems So Their Solutions Matter

Keynote Speaker

3:15-3:50PM


50 Sundar Thangapandian

University of Illinois Urbana-Champaign, Urbana, IL


Quantitative Target-specific Toxicity Prediction Model (QTTPM): A Novel Computational Toxicology Approach Integrating Molecular Dynamics Simulation and Machine Learning


02:30 – 03:45pm


51 Tessa Burch-Smith

University of Tennessee, Knoxville, TN

Professional Focused ion beam-scanning electron microscopy for three-dimensional modelling of cellular ultrastructure


11:00-11:20AM

3/30/2018 RIVERS

52 Thanh Nguyen

University of Alabama, Birmingham, AL

Student Weighted in-network Node Expansion and Ranking (WINNER): a New Approach to Identify Potential Biomarkers


9:50-10:05AM

3/30/2018 DELTA

53 Ujwani Nukala


Student Development of novel vitamin E analogs as potent radioprotectors


10:05-10:20AM

3/30/2018 FOOTHILLS

Page 27 of 44

54 Wei Tan Mississippi State University, Starkville, MS

Professional Effects of Ethanol on Escherichia coli-mediated sepsis: Differences Between Changes in Gene Expression Early and Late in the Course of Infection.


10:20-10:35AM

3/31/2018 DELTA

55 Wei Zhuang


Professional A Nonparametric Statistical Method for Detection of Serum microRNAs Biomarkers with Complete and Incomplete qPCR Data


12:05-12:20PM

3/30/2018 DELTA

56 Weida Tong


Professional A decade of MAQC effort and its contribution to our understanding of high-throughput genomics technologies

Keynote Speaker

11:30-12:20PM


57 Wenjun Bao

JMP Life Sciences, SAS Institute, Cary, NC

Professional Advanced Data Analytics using Jmp Genomics

Workshop - 1: Advanced Data Analytics using Jmp Genomics

1:30-3:15PM

3/30/2018 FOOTHILLS

58 William J Welsh

Rutgers University, New Brunswick, NJ

Professional Informatics Tools for Big Biologicals and Small Drug Molecules

Keynote Speaker

9:00-9:50AM


59 William Mattes


Professional Systems Biology and Big Data: Little Mitochondria as a Big Example


11:00-11:20AM

3/30/2018 FOOTHILLS

60 William Sanders

IT Research and Cyberinfrastructure, Hartford, Connecticut

Professional MCBIOS Timber Rattlesnake Genome Project: Current Status and Lessons Learned

Session - 9: MCBIOS Group Projects

10:50-11:15AM

3/31/2018 FOOTHILLS

61 Yan Li Bennett Professional Distinguishing Session - 2: 10:05- 3/30/2018 DELTA

Page 28 of 44

Aerospace, Cary, NC

Resistance-Conferring from Susceptible Mutations in Acetohydroxyacid Synthase by High Performance Computing-Enabled Computational Modeling

Next generation tools for environment and health research

10:20AM

62 Ying Wang Mississippi State University, Starkville, MS

Professional Applying multiple transcriptome analyses to understand plant-viroid interactions


10:05-10:20AM

3/30/2018 RIVERS

63 Zhichao Liu National Center for Toxicological Research, US FDA, NCTR

Professional Unraveling Gene Fusion Events in Neuroblastoma for Precision Medicine


11:35-11:50AM

3/30/2018 DELTA

64 Zongliang Yue

University of Alabama, Birmingham, AL

Student WIPER: Weighted in-path edge ranking for biomolecular association networks


11:05-11:20AM

3/31/2018 RIVERS

Page 29 of 44

MCBIOS 2018 Conference Proceedings

MCBIOS 2018 presenters who had their poster or platform abstracts accepted for presentation are eligible to submit a full paper on the work they presented to be considered for formal, peer-reviewed publication in the conference proceedings. The proceedings will appear in a special issue of BMC Bioinformatics. Past MCBIOS Proceedings have yielded an average impact factor of 5.17 (2006-12), which speaks strongly of the impact of MCBIOS and its participants in bioinformatics. The deadline for submission of these papers is Saturday, April 30th, 2018.

BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. Submissions must be within this scope of interest and represent original work. Important note: Like last year, BMC has requested that we restrict acceptance to the top 14 papers. As such, MCBIOS will officially recognize the best paper from among those submitted and highlight it in the MCBIOS Proceedings editorial. This best paper will also be eligible to be recognized in the Highlights Track for the 2015 ISMB Proceedings.

Specific formatting instructions for Proceedings papers can be found on their website (http://www.biomedcentral.com/info/authors/instprepdoc). Authors of accepted papers will be asked to pay an article-processing charge of £730 (about USD 913 at current exchange rates), an amount discounted for this event from the standard $2,145 cost. Because this is a particular issue, fee waivers and institutional discounts do not apply.

If you intend to submit a paper, please send your tentative title/abstract to the Senior Editor, ([email protected]) as soon as possible to enable us to better plan for reviews, paper handling, etc. Papers should be submitted by email to the Senior Editor.

Timeline:

April 28, 2018 – Manuscripts should be e-mailed to Jonathan Wren

May 23, 2018 – Reviewers return comments to editors

June 13, 2018 – Revisions due back from authors

June 26, 2018 – Final decisions made on submitted papers by reviewers

July 3, 2018 – Editors notify authors of acceptability of papers

July 28, 2018 – All final manuscript revisions due to editors along with

payment of article processing charges due to MCBIOS.

Page 30 of 44

http://www.biomedcentral.com/bmcbioinformatics/

http://www.biomedcentral.com/info/authors/instprepdoc

mailto:[email protected]


Biographies

Dr. Bindu Nanduri, Ph.D., MCBIOS President and MCBIOS 2018 Conference Co-Chair Associate Professor, Department of Basic Sciences, Mississippi State University Email: [email protected] Dr. Nanduri is an Associate Professor in the College of Veterinary Medicine and a Fellow at the Institute for Genomics Biocomputing and Biotechnology at Mississippi State University. She has a PhD in Biochemistry and Molecular Biology from the University of Arkansas for Medical Sciences. Her research interests include studying the intersection of polyamine metabolism and pneumococcal virulence, understanding bacterial-viral synergy in bovine

respiratory disease, annotation of active kinases and deubiquitinases in the chicken genome and developing bioinformatics resources for agricultural species.

Dr. Daniel G. Peterson, Ph.D. – MCBIOS 2018 Conference Co-Chair Director of the Institute for Genomics, Biocomputing & Biotechnology (IGBB) and Professor in the Department of Plant & Soil Sciences, Mississippi State University E Mail: [email protected] Dr. Daniel G. Peterson is director of the Institute for Genomics, Biocomputing & Biotechnology (IGBB; www.igbb.msstate.edu) and a professor in the Department of Plant & Soil Sciences at Mississippi State University. Peterson’s research is focused on understanding the biomolecular interactions underlying the diversity, value, and sustainability of species of

agricultural, medical, bioenergy, and/or ecological importance. Peterson has co-authored >60 peer-reviewed papers including publications in Nature, Science, and Nature Biotechnology. During his career, Peterson has received funding from the NSF, USDA, DOD, and NIH. He has twice received the Mississippi Agricultural & Forestry Experiment Station Grantsmanship Award, and in 2013 he was awarded the Ralph E. Powe Research Excellence Award, the highest research honor bestowed by MS State. Peterson has served as major advisor to six postdocs, six Ph.D. students, and two M.S. students. In addition, he has served on 49 graduate student committees. In his role as IGBB director, Peterson is in charge of all aspects of IGBB operations including financial oversight, public relations, scientific vision, facility operation, and regulatory compliance. Peterson is active in the International Cotton Genome Initiative (ICGI) and has served on the scientific policy committee of the American Society of Plant Biologists (ASPB). He is an associate editor for Gene and Plant Gene and on the editorial board of Analytical Biochemistry.

Dr. Andy Perkins, PhD. – MCBIOS 2018 Conference Co-Chair Associate Professor, Department of Computer Science, Mississippi State University Email: [email protected] Dr. Perkins is an Associate Professor of Computer Science and Engineering. Dr. Perkins joined Mississippi State University in 2008 after completing his PhD in Computer Science at the University of Tennessee. His research interests are in the areas of computational biology and bioinformatics, graph algorithms, and high performance computing. Dr. Perkins previously served on the MCBIOS board of

directors and as the tenth president of the organization. At Mississippi State University, he serves as the chair of the steering committee for the Certificate in Computational Biology and co-director of the Digital Biology Learning Community. Dr. Perkins is a Senior Member of the Association for Computing Machinery.

Page 31 of 44




Dr. Shraddha Thakkar, Ph.D. – MCBIOS 2018 Program Co-Chair Visiting Scientist, Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR Email: [email protected]

Dr. Thakkar works at FDA’s National Center for Toxicological Research. Her research interests are in applying bioinformatics and cheminformatics for study of toxicity and drug development with specific interest in drug-induced liver injury. She has received multiple research and leadership awards regionally and nationally and with FDA. That includes Genentech Innovation in Biotechnology Award from American Association of Pharmaceutical Scientist (AAPS), Margret C. Etter Student lecturer award from

American Crystallography Association, and Outstanding Service award from FDA. Dr. Thakkar has adjunct appointments at both University of Arkansas for Medical Sciences and University Arkansas at Little Rock (Assistant Professor). Furthermore, Dr. Thakkar was elected as Board member of the Mid-South Computational Biology and Bioinformatics Society (MCBIOS) in 2014 and served as President for the Society from 2016-2017. She is also the Chair of Pharmacogenomics Group at AAPS.

Dr. Prashanti Manda, Ph.D. – MCBIOS 2018 Program Co-Chair Assistant Professor, Department of Computer Science University of North Carolina at Greensboro Email: [email protected] Prashanti Manda is an Assistant Professor in the department of Computer Science where she teaches Advanced Data Structures and Bioinformatics. Dr. Manda’s research interests are in Natural language processing (NLP), Bioinformatics, and Data analytics. She earned a BE in Computer Science and Engineering from India and a PhD. in Computer Science and Engineering from Mississippi State University. Her research has focused on developing algorithms for data mining and data analytics applied to large

data stores of biological ontology data. At UNC Chapel Hill, Dr. Manda has developed semantic similarity algorithms for scalable comparison of evolutionary phenotypes using ontology semantics. With funding from Microsoft Azure research in 2017, she is conducting a Big Data analysis of approximately 155 million publication records to quantify the impact of scientific research across domains.

Dr. Mary Yang, Ph.D. – MCBIOS 2018 Program Co-Chair Associate Professor, University of Arkansas Little Rock Email: [email protected] Dr. Mary Yang is an Associate Professor at UALR and Director of the MidSouth Bioinformatics Center and the UALR-UAMS Joint Bioinformatics MS/Ph.D. Program. After completing MSECE, M.S., and a Ph.D. degree supported by a Bilsland Dissertation Fellowship at Purdue University, she joined the National Human Genome Research

Institute at the NIH. During her tenure there, she made contributions to large-scale genomics and systems biology research projects, and was Founding Editor-in-Chief of International Journal of Computational Biology and Drug Design, a NIH PubMed indexed journal. She is on the editorial broads of The Journal of Supercomputing and International Journal of Pattern Recognition and Artificial Intelligence. She has published over 50 PubMed-indexed articles and 70 DBLP-indexed computer science papers. Dr. Yang's main research interest is in developing functional genomics and systems biology-based approaches that render a better understanding of the molecular mechanisms underlying complex diseases.

Page 32 of 44




Dr. Cesar M. Compadre, Ph.D., - MCBIOS 2018 Finance Coordinator Professor, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little rock, AR Email: [email protected] Dr. Compadre is a professor at the Department of Pharmaceutical Sciences, of the University of Arkansas for Medical Sciences. He has extensive research experience on the development of bioactive compounds based on naturally occurring compounds, and on the use of molecular modeling in drug design and structure-activity studies. He has published over 90 papers and co-authored more than 70 patents related to the development of bioactive compounds. He is also the

developer of one FDA approved antimicrobial technology, which is commercially used, and he is also co-founder of Tocol Pharmaceuticals, a company focused on the development of enhanced vitamin-E analogues. Dr. Compadre has extensive International research collaborations in Drug Discovery, Global Health and Phytopharmaceuticals. Dr. Compadre has a BSPharm degree, and obtained his Ph.D. degree in medicinal chemistry and pharmacognosy, from the University of Illinois at Chicago. He conducted postdoctoral research on structure-activity relationships studies using molecular modeling at the University of Illinois working with Dr. John M. Pezzuto and at Pomona College working with Professor Corwin Hansch. Additionally, he had a sabbatical experience at NASA Ames Research Center in computer modeling.

Keynote Speakers

Dr. Russell D. Wolfinger, Ph.D. – MCBIOS 2018 Keynote Speaker I Director of Scientific Discovery and Genomics, SAS Russ Wolfinger, Ph.D., Director of Scientific Discovery and Genomics at SAS, leads a team in research and development of JMP-based software solutions in the areas of genomics and clinical research. He joined SAS in 1989 after earning a Ph.D. in statistics from North Carolina State University (NCSU). For ten years he devoted his efforts to developing statistical procedures in the areas of linear and nonlinear mixed models, multiple testing and density estimation. In 2000 he started the Scientific Discovery department at SAS. Wolfinger is a co-author of more than 100 publications and a fellow of both the

American Association for the Advancement of Science and the American Statistical Association. He also is an adjunct faculty member at NCSU and the University of North Carolina at Chapel Hill, and a leading member of the MicroArray Quality Control (MAQC) Consortium, which conducts sweeping assessments of genomics technologies and is sponsored by the US Food and Drug Administration.

Dr. Lawrence J. Lesko, Ph.D., F.C.P. – MCBIOS 2018 Keynote Speaker II Professor, Pharmaceutics, University of Florida, Lake Nona, Orlando Email: [email protected] Lawrence J. Lesko, Ph.D., F.C.P. joined the UF Research and Academic Center in Lake Nona (Orlando) in July 2011. Before joining UF, Dr. Lesko worked nearly 20 years in the Food and Drug Administration’s Center for Drug Evaluation and Research as the Director of the Office of Clinical Pharmacology. He was also Chair of the Clinical Pharmacology Coordinating Subcommittee of the FDA’s Medical Policy Coordinating Committee and authored or co-authored numerous Guidance for Industry, and started the FDA’s Voluntary Genomics Data Submission Program

and Mechanistic Drug Safety Program. Lesko has published more than 200 peer-reviewed scientific publications

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and is a frequent invited national and international speaker in clinical pharmacology, personalized medicine, pharmacometrics and systems pharmacology. His research interests include drug development and regulatory science, quantitative clinical pharmacology and pharmacogenomics. In 2011, Lesko received the Gary Neil Prize for Innovation in Drug Development from the American Society of Clinical Pharmacology and Therapeutics (ASCPT). He also received the Coriell Scientific Leadership Award for Personalized Medicine (2010), the Rawls-Palmer Progress in Medicine award from ASCPT (2007), the University of North Carolina Institute for Pharmacogenomics and Individualized Therapy Award for Clinical Service (2007), and the Nathanial B. Kwit Distinguished Service Award for Clinical Pharmacology from the American College of Clinical Pharmacology (2007). Lesko served as President of the American College of Clinical Pharmacology in 2004-2006. He is a Fellow in the Japanese Society for the Study of Xenobiotics, American College of Clinical Pharmacology and the American Association of Pharmaceutical Scientists. He is Board Certified in Clinical Pharmacology and a registered pharmacist.

Dr. Steve Jennings, Ph.D. – MCBIOS 2018 Keynote Speaker III - No Boundary Thinking Keynote Speaker and MCBIOS-NBT Joint Bioinformatics Research Workshop Organizer Professor Emeritus of Information Sciences and Bioinformatics, UALR Dr. Jennings is a Professor Emeritus of Information Science and Bioinformatics; he retired from the University of Arkansas at Little Rock (UALR) in 2014 though he still consults on a National Science Foundation Grant concerning “no-boundary thinking” through Arkansas State University. He currently resides in the Tucson area. Steve received his PhD in Computer Science from Iowa State University in

1981 and his Executive MBA degree from the University of Colorado–Denver in 1991. He started his career in 1980 as an Assistant Professor at Colorado State University and subsequently held numerous senior leadership positions in the software industry developing operating systems and networks, medical device software, web-based financial calculators, mobile communications, artificial intelligence platforms, and high-performance computing systems. He has experience in technical/project/general management, finance and operations, personnel management, marketing and sales, quality improvement, and organizational development. He consulted for several Fortune 500 companies and has been involved with many start-up companies. He has also been active with the management of several not-for-profit organizations. He returned to academia in 2002 to:

• found the first regional graduate program in bioinformatics in the south-central US (jointly sponsored by UALR and the University of Arkansas for Medical Sciences),

• found the MidSouth Bioinformatics Center at UALR, • found the MidSouth Computational Biology and Bioinformatics Society (MCBIOS), and • start up the Bioinformatics Core of the NIH IDeA Network for Biomedical Research Excellence (INBRE)

grant to Arkansas. He was inducted into the Arkansas Academy of Computing in 2013.

Dr. William J. (Bill) Welsh, Ph.D. – MCBIOS 2018 Keynote Speaker IV Norman H. Edelman Endowed Professorship in Bioinformatics, Department of Pharmacology at the Robert Wood Johnson Medical School (RWJMS), Rutgers University in Piscataway, NJ Email: [email protected] William J. (Bill) Welsh, Ph.D., holds the Norman H. Edelman Endowed Professorship in Bioinformatics in the Department of Pharmacology at the Robert Wood Johnson Medical School (RWJMS), Rutgers University in Piscataway NJ. Concurrently, he serves as Associate Director of the Division of Cheminformatics of the Biomedical Informatics Center at the Rutgers-Cancer Institute of New Jersey (R-CINJ). He also serves as a

research professor in the Department of Chemistry at Princeton University. Dr. Welsh’s laboratory specializes in the

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development and application of computational tools for drug discovery and development, cheminformatics, and pattern recognition. Active projects in drug discovery include therapeutic agents for cancer, pain management, and thrombotic conditions. His publication record includes over 500 articles in peer-reviewed books and journals, 200 abstracts for presentations at professional scientific meetings, and multiple patents and patent applications. His research has been funded by the NIH, NSF, EPA, FDA, DoD, the State of New Jersey, and various biotech and pharmaceutical companies. In October 2007, Dr. Welsh founded Snowdon, Inc., (snowdonpharma.com) a biopharmaceutical company that specializes in development and application of computational software to accelerate molecular discovery. He and his family reside in Princeton, New Jersey. Dr. Welsh received a B.S. degree in Chemistry from St. Joseph’s University (Philadelphia, PA). He earned a Ph.D. in Theoretical Physical Chemistry from the University of Pennsylvania (Philadelphia, PA). He then pursued postdoctoral studies in computational physical chemistry in the Department of Chemistry at the University of Cincinnati (Cincinnati, OH) and at the National Institutes of Health (NIH). Since 2013, Dr. Welsh has collaborated with Dr. Herschel Rabitz in the Department of Chemistry at Princeton University (Princeton, NJ) working on pattern recognition tools for complex high-dimensional multivariate problems in the biomedical arena.

Dr. Weida Tong, Ph.D. – MCBIOS 2018 Keynote Speaker V Director, Division of Bioinformatics and Biostatistics, NCTR/FDA Email: [email protected] Dr. Tong is Director of Division of Bioinformatics and Biostatistics at FDA’s National Center for Toxicological Research (NCTR/FDA). He has served science advisory board for several multi-institutional projects in Europe and USA. He also holds an adjunct appointment at several universities. Also, he is the founder and board chairperson of newly established international MAQC Society. His division at FDA is to develop bioinformatic methodologies and standards to support FDA research and regulation and to advance regulatory science and personalized

medicine. The most visible projects from his group are (1) conducting the Microarray and Sequencing Quality Control (MAQC/SEQC) consortium to develop standard analysis protocols and quality control metrics for emerging technologies to support regulatory science and precision medicine; (2) development of liver toxicity knowledge base (LTKB) for drug safety; (4) in silico drug repositioning for the enhanced treatment of rare diseases; and (4) development of various tools such as ArrayTrackTM suite to support FDA review and research on pharmacogenomics. Also, his group also specializes in molecular modeling and QSARs with a specific interest in estrogen, androgen, and endocrine disruptor. Dr. Tong has published more than 250 papers and book chapters.

Workshop Coordinators and Speakers

Dr. Wenjun Bao, Ph.D., Chief Scientist and Sr. Manager at JMP Life Sciences – MCBIOS 2018 Workshop Coordinator, SAS Advanced Data Analysis Workshop Data scientists from the SAS / JMP Life Sciences division will offer an advanced level hands-on workshop to MCBIOS Society conference attendees. During this workshop, attendees will analyze one or more complex experiments and discuss various statistical methods and concepts. Attendees will be able to follow along on their laptop. Depending on the problems, topics can include: Design of Experiments, Quality Assessment, Normalization, ANOVA and Mixed Modeling, Reproducibility, Pattern Discovery, Predictive Modeling, Genetic Marker Screening, Genome-Wide

Association Study, Population Analysis, Marker-Assisted Breeding and Cross-Evaluation, Best Linear Unbiased Prediction, Linkage Mapping, Quantitative Trait Loci, Bioassay, Clinical Trials, Bioequivalence, Method Comparison, Calibration Curves, Limit of Quantification. JMP software will be used, with dashboards created by JMP Genomics and JMP Clinical. Dr. Wenjun Bao will provide this workshop from JMP/SAS. Dr. Bao is Chief Scientist and Sr. Manager at JMP Life Sciences, SA

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Dr. Inimary Toby, Ph.D., Computational Biologist II, Dept. of Clinical Sciences, University of Texas Southwestern Medical Center – MCBIOS 2018 Workshop Coordinator, Career Development Workshop for Young Scientists Email: [email protected] The goals of this workshop are: 1) To present trainees with a breadth of career-related resources 2) To provide a framework for career trajectory and planning activities 3) To complete exploratory career tasks using media and live discussions 4) To assist trainees in creating an individualized career development plan (IDP) Topics that will be addressed include: how to navigate a postdoc, marketing as a grad

student, solving computational challenges with limited resources, goals-driven Science, and managing “big” expectations. Dr. Toby is currently a Senior Computational Scientist at the University of Texas Southwestern Medical Center in Dallas, Texas. She received her Ph.D. from the Ohio State University, College of Medicine in Biomedical Science with a concentration in Organ Systems Biology. Following that, she pursued postdoctoral training with the Genomics group at The Civil Aerospace Medical Institute in Oklahoma City. She has been the recipient of several NIH research grants during her doctoral work and subsequently received a postdoctoral research grant from the National Academies of Sciences. She has received additional fellowship awards from the American Physiological Society and participated in outreach initiatives aimed at increasing the pipeline of K-12, undergraduate and post-baccalaureate trainees into STEM careers. Her research interests include utilizing computational methods to facilitate the analysis of specialized next-generation sequence data and mainly developing strategies to enable accurate interpretation of information from open source software and data repositories.

Dr. Binsheng Gong, Ph.D., Visiting Scientist, Division of Bioinformatics and Biostatistics, NCTR/FDA – MCBIOS 2018 Workshop Coordinator, Next-Generation Sequencing (NGS) datasets analysis using Galaxy platform This workshop is for users who want to acquire the skills required to analyze the Next-Generation Sequencing (NGS) datasets using Galaxy platform. The event is open to all the students, postdocs as well as faculty members who are interested in NGS data processing and analysis with general workflows. The workshop will be a focus on the basic usage of Galaxy platform, with demos covering NGS data quality assessment, read alignment to the genome, gene expression quantification and

differential gene expression analysis. Galaxy is an open source, web-based platform for data intensive biomedical research. It provides hundreds of tools for next-generation sequencing (NGS) data analysis, including but not limited to genetic variance calling, transcriptomic profiling, DNA methylation, microbial genomics, pan-genomics, metagenomics, etc. With Galaxy, Wet-lab researchers can manage their data and do most general analysis with short-term training. Galaxy also provides a good way to make research more transparent and more accessible, and improve the reproducibility and robustness scientific research. Dr. Gong is a Visiting Scientist in Division of Bioinformatics and Biostatistics at FDA’s National Center for Toxicological Research (NCTR/FDA), with expertise in next-generation sequencing technologies and high-throughput data analysis. His studies have significantly advanced the application of bioinformatics methods and systems biology strategies in the basic biological study and translational medicine, and his research achievements have been recognized with several awards from U.S. FDA and from China. He has served as a reviewer for multiple prestigious journals such as Oncotarget, PLoS ONE, Scientific Reports, etc. Dr. Gong has been involved as one of the major investigators in the FDA led SEquencing Quality Control (SEQC) project, and he is the leading author of one Nature Biotechnology paper and co-authors of several others produced by SEQC project. Dr. Gong has more than 30 research papers published in prestigious journals such as Nature Biotechnology, Genome Biology, Nucleic Acid Research, etc. His researches have received more than 350 citations from government agencies, armies, pharmaceutical and food companies and research

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institutes. Dr. Gong was one of the chapter editors of the first bioinformatics text book for higher institutions in China.

Dr. Sorina C. Popescu, Ph.D. – MCBIOS 2018 Break out Session: I and IV Organizer Assistant Professor, Mississippi State University Email: [email protected] Dr. Popescu is currently Assistant Professor at the Mississippi State University of MS, in the Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology. She earned her Ph.D. in Plant Biology from Rutgers the State University of New Jersey in 2003. After completing her Ph.D., Dr. Popescu has accepted a position as a postdoctoral associate at Yale University in New Haven, CT, where she explored new advances in plant

–omics techniques. During that time, she developed protein microarrays and new methods for the characterization of plant networks. Her postdoctoral research put her on a path that she still follows today – utilization of ‘omics’ techniques to identify and study signal transduction networks in plants. Dr. Popescu’s current work focuses on kinases and signaling pathways activated by pathogens in model experimental systems, and high-throughput methods to characterize protein activities and interactions with other molecules. Her work has led to an understanding of the composition and topology of plant immune-related signaling networks. A strong motivation of translating knowledge accumulated in model plant systems to crops has led to Dr. Popescu to expand the repertoire of studied plant systems to include tomato, sweet potato, and cotton. Dr. Popescu is also interested in exploring topics related to the plant environmental stress responses and biotechnology-directed applications of her research. Dr. Popescu has authored over 20 peer-reviewed publications, thematic reviews, and book chapters. She presented her work at numerous national and international scientific meetings and workshops.

Dr. Marilyn Warburton, Ph.D. – MCBIOS 2018 Break out Session: I Featured Speaker Corn Host Plant Resistance Research, United States Department of Agriculture Email: [email protected] Marilyn Warburton is from Tucson, Arizona, and obtained a BS and MS in plant breeding at the University of Arizona. She studied plant genetic diversity and molecular genetics with Dr. Fred Bliss at the University of California, Davis and subsequent postdoctoral and sabbatical work at UCDavis, the University of Illinois, and Cornell University. In her current work, Warburton seeks to identify and use natural allelic diversity in maize to solve problems in biotic and stress resistance. She worked for 10 years at the International Maize and Wheat Improvement Center, where she worked on the measurement of genetic diversity in

maize and wheat to study constraints to conservation and use of plant genetic resources, and document gene flow between crops and wild relatives. She also worked on identification of maize genetic sequences associated with drought tolerance and provitamin A, which now allow breeders to improve maize nutrition via marker assisted selection. Currently, Warburton works in the Corn Host Plant Resistance Research Unit of the USDA Agriculture Research Service, where she and colleagues work to identify and validate genetic sequences associated with resistance to the toxic fungi and lepidopteran insects.

Dr. Natàlia Garcia-Reyero, Ph.D. – MCBIOS 2018 Featured Speaker and Break out Session: II Organizer Research Biologist, US Army Engineer Research and Development Center, Vicksburg MS. Email: [email protected] Dr Natàlia Garcia-Reyero is a Research Biologist at the US Army Engineer Research and Development Center in Vicksburg MS. The principal focus of her research is on understanding the impacts and sub-lethal effects of contaminants and other stressors on water quality, aquatic and terrestrial organisms, and ecosystem health. She also involved in

different fields such as paleogenomics or metagenomics. She is an Adjunct Professor at Institute for Genomics Biocomputing and Biotechnology from Mississippi State University.

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mailto:[email protected]?Subject=From%20ARS%20website


Dr. Robert J. Doerksen, Ph.D. - MCBIOS 2018 Featured Speaker and Break out Session: III Organizer Associate Dean of the Graduate School, Associate Professor of Medicinal Chemistry and Research Associate Professor in the Research Institute of Pharmaceutical Sciences Email: [email protected] Robert J. Doerksen was born in Winnipeg, Manitoba, Canada and spent time growing up in Madison, Wisconsin, USA; Fredericton, New Brunswick, Canada; and Cambridge, England, UK. He obtained a Double First Class Honours Bachelor of Science in Mathematics and Physics from University of New Brunswick (UNB), a graduate level Diploma in Christian Studies from Regent College in Vancouver, British Columbia, Canada, and a PhD in Chemistry from UNB, under the guidance of Prof. Ajit Thakkar,

specializing in computational physical chemistry. He proceeded to postdoctoral fellowships in the Department of Chemistry at University of California, Berkeley, with Prof. Martin Head-Gordon, and in the Department of Chemistry at University of Pennsylvania (Philadephia, PA, USA), with Prof. Michael Klein. Since 2004, he has been at the School of Pharmacy at the University of Mississippi in Oxford, MS, USA, first as an assistant professor in the Department of Medicinal Chemistry and currently as an associate professor of medicinal chemistry in the Department of BioMolecular Sciences. Doerksen also is a research associate professor in the Research Institute of Pharmaceutical Sciences at the University of Mississippi. In 2017, he was appointed as Associate Dean of the Graduate School.

Dr. Tessa Burch-Smith, Ph.D. – MCBIOS 2018 Featured Speaker and Break out Session: IV Organizer Assistant Professor, Biochemistry & Cellular and Molecular Biology, University of Tennessee at Knoxville Email: [email protected] Dr. Tessa Burch-Smith completed her Ph.D. thesis with Dr. S.P. Dinesh-Kumar at Yale University, studying how plant Resistance proteins detected the presence of pathogen-derived molecules during the plant innate immune response. She then conducted post-doctoral research with Dr. Patricia Zambryski at the University of California, Berkeley. The focus of her post-doctoral studies was the regulation of intercellular trafficking

mediated by plasmodesmata. This work led to intriguing findings about the role of chloroplasts in controlling not only intercellular trafficking but also plasmodesmata development. At UC Berkeley, she developed interest in electron microscopy as a tool for studying plasmodesmata ultrastructure. Since joining the faculty of the Department of Biochemistry & Cellular and Molecular Biology at the University of Tennessee, Knoxville she has continued to study the plasmodesmata-chloroplast relationship. As a complement to transmission electron microscopy for studying plasmodesmata ultrastructure, lab has adopted focused ion beam-scanning electron microscopy (FIB-SEM) to study plasmodesmal and organelle distribution in relatively large cell volumes. Dr. Burch-Smith currently serves as a Senior Editor at the journal Molecular Plant-Microbe Interactions (MPMI).

Dr. Brian Counterman, Ph.D. – MCBIOS 2018 Featured Speaker and Break out Session: V Organizer Associate Professor, Department of Biological Sciences, Mississippi State University Email: [email protected] Dr. Brian Counterman is currently an Associate Professor in the Department of Biological sciences at Mississippi State University. Brian’s research takes an integrative approach to studying the origin of novel adaptive traits and new species. His research leverages the amazing diversity of butterfly wing colors to better understand the evolution and development of pattern formation. His background is in population genetics, which he has used to identify the genes

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responsible for butterfly color pattern variation. He is part of large international collaboration of researchers that use neotropical Heliconius butterflies as a model system to study biological variation. Brian’s work on these butterflies is truly integrative, involving a mix of extended field collections in South America, sequencing of hundreds of butterfly genomes, developmental of image analytical methods, genome editing of laboratory butterflies, all followed by extensive computational analyses. Brian brings over 15 years of experience and federal funding for butterfly genome research. He has published over 25 peer-reviewed publications, given over 30 invited seminars and served on several advisory boards for genome consortiums

Dr. William B. Mattes, PhD, DABT – MCBIOS 2018 Featured Speaker Break out Session: VI Director, NCTR/OR/DSB Email: [email protected]

Dr. Mattes is the Director of the Division of Systems Biology, part of the FDA’s National Center for Toxicological Research. He has been an independent consultant as well as Director of Toxicology at the Critical Path Institute where he developed and directed the Predictive Safety Testing Consortium (PSTC), a collaboration of the world’s major pharmaceutical companies, with FDA and EMEA advisors. This work resulted in the establishment of a formal process of FDA/EMA biomarker

qualification. Dr. Mattes also developed the COPD Biomarkers Qualification Consortium. Dr. Mattes other positions included senior scientific director of Toxicogenomics at Gene Logic, Associate Director of Toxicogenomics and Group Leader of Genetic Toxicology at Pharmacia Corp, Kalamazoo, MI, Group Leader of Experimental Toxicology and Metabolism at Ciba Pharmaceuticals, Summit, NJ, and Group Leader of Molecular and Cellular Toxicology, Ciba-Geigy Agricultural Chemical Division, Farmington, CT. Dr. Mattes received a BA from the University of Pennsylvania and PhD in biological chemistry from the University of Michigan, Ann Arbor. He did his postdoctoral training at the Johns Hopkins University, and was a staff fellow at the National Cancer Institute. In 1997 Dr. Mattes became a diplomate of the American Board of Toxicology. He is a full member of the Society of Toxicology and the American College of Toxicology (ACT). His service to these organizations includes Secretary-Treasurer, and then President of the SOT’s Molecular Biology Specialty Section; two terms on the SOT’s Continuing Education Committee (and development of a standards CE booklet); service on the ACT’s Program and Website Committees, currently on ACT’s Council, and former Secretary of the Roundtable of Toxicology Consultants. His research interests include bioinformatics, data science, cross-species and cross-tissue comparisons of molecular responses, as well as group dynamics that lead to successful collaboration between scientists and changes in scientific policy. He also currently fills the guitar chair for the group Jazzicology at the ACT’s annual meeting.

Dr. Minjun Chen, Ph.D.- MCBIOS 2018 Break out Session: VI Organizer Principal Investigator, NCTR/DBB, Jefferson, AR Minjun Chen received his B.Sc (1997) and Ph.D. (2003) from Zhejiang University, Hangzhou, China. He worked as an assistant and then associate professor in the school of pharmacy, Shanghai Jiaotong University, Shanghai. He also worked as a postdoctoral fellow for University of Medicine and Dentistry of New Jersey (UMDNJ) in Piscataway, New Jersey and the FDA's national center for toxicological research (NCTR) in Jefferson, Arkansas. Currently,

Dr. Chen is a principal investigator working at the Division of Bioinformatics and Biostatics of the FDA’s NCTR and serve as the adjunct faculty and mentor for the bioinformatics program joint by Univ. of Arkansas at Little Rock (UALR) and Univ. of Arkansas for Medical Sciences (UAMS). He received the FDA award for outstanding junior investigator (2012) and the NCTR scientific achievement award (2014). He and Dr. Eileen E Navarro Almario (CDER/OCS) launched the FDA Liver Toxicity Interest Group in 2014, and now the group has been endorsed by the FDA’s Office of the Chief Scientist as an official working group including > 60 members of FDA scientists with interest and expertise in liver toxicity or liver diseases. Currently, he is the editor together with Dr. Yvonne Will (Pfizer) to create a Springer book titled “Drug-Induced Liver Toxicity”. He also served as the editorial board members for the journals including PeerJ, Chinese herb medicine and as the reviewers for journals. His primary

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research interests encompass drug-induced liver injury, biomarker discovery, bioinformatics, and toxicogenomics. Dr. Chen has authored or co-authored more than 70 book chapters or scientific publications in the prestigious journals such as Gastroenterology, Hepatology and Journal of Hepatology. His current research focus is in two areas: (1) development of the Liver Toxicity Knowledge Base (LTKB) to address the public health concerns related to drug-induced liver injury, and (2) identification of predictive biomarkers for the prognostics and predicting the outcome of chemotherapy of breast cancer patients for personalized medication.

Dr. Rakesh Kaundal, Ph.D. – MCBIOS 2018 Featured Speaker Break out Session: VII Director, Bioinformatics Facility, Utah State University Before joining the Utah State University as Director of bioinformatics facility, Rakesh Kaundal was the Director of High-Performance Computing and Bioinformatics Facility at the Institute for Integrative Genome Biology (IIGB / CEPCEB), University of California, Riverside. His major role is to lead / manage the UCR’s HPC infrastructure, supervise informatics staff, instruct bioinformatics workshops and develop data analysis pipelines for high-throughput data analysis, including data from next generation sequencing (NGS) technologies.

Dr. Zhichao Liu, Ph.D., MCBIOS 2018 Break out Session: VII Organizer Principal Investigator, Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR Dr. Liu received his Ph.D. degree from Nankai University, China. Currently, he is a Visiting Scientist in Division of Bioinformatics and Biostatistics (DBB), National Center of Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA). In past ten years, he led or took part in several cutting-edge projects from both industry and academia. Recently, Dr. Liu focused on developing the standard pipeline to balance the efficacy and safety in drug repositioning and drug safety areas. The goals aims at providing the standard

in silico pipeline for drug repositioning and early drug safety detection by retrieving, integrating and organizing the information from chemical, biological and clinical spaces, which help industry to seek for the optimal route to accelerate the drug development efficacy from advanced regulatory sciences perspective.

Dr. Stephen B. Pruett, B.S., Ph.D. – MCBIOS 2018 Featured Speaker and Break out Session: VIII Organizer Department Head, Department of Basic Sciences, Mississippi State University Email: [email protected] Dr. Stephen B. Pruett received his Ph.D. in Immunology from LSU School of Medicine in Shreveport in 1980 and did postdoctoral training in the laboratory of Dr. J. Claude Bennett, M.D., in 1980-1982 at the University of Alabama in Birmingham. His first academic research position was at Mississippi State University, where he rose from Assistant Professor (1984)

to Professor (1991). He moved back to LSU School of Medicine in Shreveport as a Professor from 1997-2007, and in 2007 he accepted a position as Department Head of the Department of Basic Sciences in the College of Veterinary Medicine at Mississippi State University. Dr. Pruett has served on more than 30 NIH grant review panels and was a regular member of the Innate Immunity and Inflammation Study Section from 2010-2014. He has served on the editorial boards of several journals and currently serves on the boards of Toxicology and Applied Pharmacology and Alcohol. Dr. Pruett has published more than 125 peer-reviewed publications and has obtained approximately $19,000,000 in competitive research funding. His primary research interests include: mathematical and statistical modeling of the immune system, chemical mediated neuroendocrine stress responses and their effects on the immune system, the effects of ethanol on the immune system, and the role of redox status on immune function.

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Dr. William S. (Shane) Sanders, Ph.D. – MCBIOS 2018 Workshop Coordinator and Break out Session: IX Organizer Manager, IT Research Cyberinfrastructure, The Jackson Laboratory E-mail: [email protected] Dr. Sanders is the Manager for Research Cyberinfrastructure in the Information Technology Department at The Jackson Laboratory (JAX). At JAX, he facilitates collaborative research with JAX faculty at campuses in Bar Harbor, ME, Farmington, CT, and Sacramento, CA, all while overseeing the high-performance computing, cloud computing, and data storage and management resources in the research environment. Dr. Sanders received a BS in

Biochemistry and a BS in Computer Science from Mississippi State University in 2003. He received his PhD in Molecular Biology from Mississippi State University in 2011, where he focused on computational biology, proteomics, and machine learning. His postdoctoral training focused on computational genomics and evolutionary biology in agricultural species, and he is currently a PhD candidate in Computer Science focusing on high performance computing and modeling. Dr. Sanders has authored multiple publications in these research domains, and has served as the Bioinformatics Section Editor for Genomics, Proteomics, and Bioinformatics, the official journal of the Beijing Institute of Genomics, the Chinese Academy of Sciences, and the Genetics Society of China. He is the organizer of the annual Evolution of Genome Size workshop at the International Plant and Animal Genome (PAG) conference, serves on the technical committee for the Practice and Experience in Advanced Research Cyberinfrastructure (PEARC) conference, and is actively involved in the NSF Extreme Science and Engineering Discovery Environment (XSEDE) initiative. His research interests include algorithm development and design, genomics, proteomics, high-performance computing, machine learning, autonomous systems, and evolutionary biology. Dr. Sanders has been involved with the MCBIOS community since MCBIOS IV in 2007.

Dr. Ping Gong, Ph.D. –MCBIOS 2018 MCBIOS-JMP Young Scientist Excellence Award Coordinator Research Biologist, Environmental Laboratory, US Army Engineer Research and Development Center, US Army Corps of Engineers, Vicksburg, MS Email: [email protected] Dr. Gong is a Principal Investigator with multidisciplinary expertise in environmental genomics, bioinformatics, bioengineering, mechanistic and predictive toxicology, and molecular modelling. He earned a Bachelor‘s degree in Environmental Biology and Ecology from Peking University and a PhD in Environmental Toxicology from the Institute

of Applied Ecology, Chinese Academy of Sciences. He completed his postdoctoral studies in the Technology University of Berlin (TU Berlin), Swedish University of Agricultural Sciences (SLU), and Biotechnology Research Institute of National Research Council of Canada. As a research biologist, he has initiated and led to completion more than 20 military and civil works projects. Findings from these projects have greatly improved the fundamental and mechanistic understanding underlying the observed toxicities of military unique and other environmental contaminants. His current research interests focus on mode of action-guided predictive toxicology, genetic variations-conferred herbicide resistance, epigenetics-driven transgenerational inheritance of phenotypic traits, and synthetic biology-based bioengineering and biocontrol of invasive species. Dr. Gong was a founding member of the Global Soils Advisory Group in the Society of Environmental Toxicology and Chemistry and served on its Steering Committee. By serving on graduate committees, he has advised more than 18 PhD and MSc students. He has published over 75 peer-reviewed research articles and book chapters and served on several editorial boards, including Frontiers in Genetics, Environmental Toxicology and Chemistry, and Korean Journal of Environmental Biology. He was elected to the MCBIOS Board of Directors in 2015.

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Dr. George Popescu, Ph.D. – MCBIOS 2018 Poster Award Coordinator Assistant Research Professor, Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University Email: [email protected] Dr. Popescu is an Assistant Research Professor at the Institute for Genomics, Biocomputing & Biotechnology (IGBB) and an adjunct assistant professor in the

Biochemistry Department at Mississippi State University. Before joining IGBB he was senior research associate the Boyce Thompson Institute, Cornell University, where he developed a bioinformatics and computational biology research direction and a senior research scientist at the National Institute for Laser, Plasma and Radiation Physics (http://www.inflpr.ro/). He received a Diploma of Engineering from the University “Politehnica” Bucharest (UPB) in 1993 and joined the university as a junior faculty member in the area of image analysis, information theory and machine learning. He received his PhD in 2001 from Rutgers University. Between 2001 and 2004 he was a Research Staff Member at the IBM TJ Watson Center in the system analysis and optimization group. In 2004 he joined the Center of Excellence in Genomics Sciences at Yale University as a postdoctoral researcher, specializing in bioinformatics and computational biology. He then joined UPB as a senior research scientist and co-organizer of an EU-funded advanced master program in imaging, bioinformatics and complex systems (http://items.pub.ro/index_en.html). One of his key research contributions was the discovery of the complex structure of the MAPK signaling networks in plants. Another significant contribution was the development of methodology for high-throughput genomics analyses, focusing on discovery of copy number variations in the human genome and development of computational and analytical tools for comparative genomics. He has recently directed a consortium investigating the activity of several classes of newly synthesized anti-microbial resistance drugs using molecular modeling and simulation methods, focusing on developing novel methods for large-scale studies of the relationship between structure and function of anti-microbial resistance drugs. He is a senior member of ACM, and a member of ISCB, SIAM, SPIE and EPS.

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http://www.inflpr.ro/

http://items.pub.ro/index_en.html

16th MidSouth Conference on

Bioinformatics & Computational Biology in conjunction with

UAB 3rd Annual Translational & Transformative

Informatics Symposium

March 28th to 30th, 2019

University of Alabama at Birmingham

Birmingham, AL

http://mcbios.org/

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Dear Hossam Abdelhamed,


Conference program is available on Meeting application app.

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