Purdue University
Vice President, Office of Research
Bioinformatics Core


Indiana University
University Information Technology Services
Department of Biology
School of Informatics and Computing

University of Michigan, Dept of Computational Medicine and Bioinformatics


The Research Division
of Ohio University

Department of Computer Science and Engineering
Eck Institute for Global Health
Complex Networks Lab
University of Notre Dame



Cincinnati Childrens’s Hospital Medical Center
Division of Biomedical Informatics, University of Cincinnati


Faculty of 1000




University of Michigan Bioinformatics Core



Purdue University

Agricultural Research

Great Lakes Bioinformatics Conference 2015


SCHEDULE (As of May 17, 2015. Subject to change without notice): There are TWO poster sessions at GLBIO: A and B.

Poster Sessions A - Tuesday, 5:30pm - 7:00pm

Poster 1
Identification of novel therapeutics for complex diseases from genome-wide association data
Mani P. Grover, Sara Ballouz, Tamsyn Crowley, R.A. George, Craig Sherman, and Merridee Wouters

Poster 3
PyMine: a PyMOL plugin to integrate and visualize data for drug discovery
Rajan Chaudhari and Zhijun Li

Poster 5
GROM: Parameter and coordinate file editor for GROMACS
Hovakim Grabski

Poster 7
Genome-scale identification and characterization of moonlighting proteins
Ishita Kamal Khan and Daisuke Kihara

Poster 9
Global versus local biological network alignment: which one is better?
Lei Meng, Aaron Striegel, and Tijana Milenkovic

Poster 11
GREAT: GRaphlet Edge-based network AlignmenT
Joseph Crawford and Tijana Milenkovic

Poster 13
Network-based protein function prediction: implications for aging
Fazle Faisal, Han Zhao, and Tijana Milenkovic

Poster 15
Chemical modification of tryptic peptides enhances peptide identification in shotgun proteomics
Sujun Li, Predrag Radivojac, Haixu Tang, Aditi Dabir, Santosh Misal, and James Reilly

Poster 17
Inferring the structural functional and phenotypic consequences of amino acid substitutions
Vikas Pejaver, Sean Mooney, and Predrag Radivojac

Poster 19
MMiRNA-Tar: A correlation and target prediction analysis tool for microRNA and mRNA expression datasets
Yang Liu, Cameron Meyer, Joshua Stolz, Gary Stuart, and Yongsheng Bai

Poster 21
PhyloPro2.0: web-based tools for the generation and visualization of phylogenetic profiles and domain architectures across Eukarya
Graham Cromar, Anthony Zhao, Xuejian Xiong, Swapna Seshadri, Noeleen Loughran, and John Parkinson

Poster 23
ORFanFinder server: toward automated identification of taxonomically restricted orphan genes
Yanbin Yin and Alex Ekstrom

Poster 25
Population scale human genome analysis on the cloud
Peter White

Poster 27
An integrative approach for gene annotation
Rasiah Loganantharaj

Poster 29
Modeling predicts NADPH oxidase complex structure modifications due to SLE-associated NCF2 mutations

Don Armstrong Miriam Eisenstein Raphael Zidovetzki and Chaim Jacob

Poster 31
Developing a new in silico pipeline for faster drug discovery
Jonathan Chen and Donald P. Visco Jr.

Poster 33
Trending topics in Bioinformatics: tracking changes over time and space
Nanda Kishore, Adapa Parvathi Chundi, and Dario Ghersi

Poster 35
Location prediction and phylogenetic analysis of miRNA in avian genome
Mustafa Broachwala and Dr. Sushma Reddy

Poster 37
Identification of signature sequences for molecular detection and identification of foodborne pathogens
Mark Mammel, Isha Patel, Jayanthi Gangiredla, David Lacher, Keith Lampel, and Chris Elkins

Poster 39
Eliciting epidemiological characteristics of H5N1 endemic in waterfowl
Neil Giridharan and Dhananjai Rao

Poster 41
A hirerachical Bayesian model for differentially expressed isoform detection from multiple biological replicates
Yifan Yang, Hao Peng, and Yuan Qi

Poster 43
VirusLand: Expedient processing of viral metagenomes from assembly to analysis
Joshua Haselton

Poster 45
Which anopheles mosquito genes are most important in promoting malaria transmission?
Yosi Shibberu, Geletaw Sahle, Zelalem Hailu, Abebe Asale, and Alemayehu Shiferaw

Poster 47
Palindromic enrichment of CRISPRs in metagenomic data sets
Abraham Moller and Chun Liang

Poster 49
MPatViewer: a MATLAB pattern viewer for DNA or RNA sequences that utilizes primer numbers
Sutharzan Sreeskandarajan, Abraham Moller, Kai Wang, John Karro, and Chun Liang

Poster 51
Structural analysis of B-cell epitopes to guide vaccine design
Saba Ferdous and Andrew Martin

Poster 53
Data pooling to identify differentially expressed genes in lung cancer of nonsmokers
Nicole Carr and Sadik Khuder

Poster 55
Identification of novel carbon transport genes in maize using bulked segregant analysis and next-generation sequencing

David Huizinga and Clifford Weil

Poster 57
Understanding stop loss, stop gain, and frameshift mutations

Kymberleigh Pagel, Vikas Pejaver, Guan Ning Lin, Lilia Iakoucheva, Sean Mooney, and Predrag Radivojac

Poster 59
Genomic and proteomic analysis of propane degradation pathways in bacterial strains
Hisako Masuda and Peter Tupa

Poster 60
Parallel algorithms for fuzzy cell classification
Samuel Schmidt and Jeremy Cox

Poster 61
Application of semi-supervise learning in Genome Wide Association Studies (GWAS) for melanoma
Hima Bindu Yalamanchili, Michael L. Raymer and Michael P. Markey

Poster 63
New metrics for learning and inference on sets and functions
Ruiyu Yang, Jovana Kovacevic, Matthew Hahn, Elizabeth Housworth, andPredrag Radivojac

Poster 65
On optimizing a computational pipeline for analysis of lung microbiome
Jeremy Cox, Melanie Cushion, and Aleksey Porollo

Poster 67
Epigenetics information improves genome wide motif discovery
Yichao Li and Lonnie Welch

Poster 69
Analysis of gene expression data in cancer patients
Thomas Wynn

Poster 71
Studying the role of two component regulatory systems in virulence regulation in streptococcus pyogenes and staphylococcus epidermidis
Alexander Thorman, Andrew Herr, Jarek Meller, and Malak Kotb

Poster 73
Inferring gene interactions using Bayesian networks
Anthony Deeter

Poster 75
Modeling the interaction interface of the TBEV restriction factor TRIM79α and the flavivirus NS5
Heather Brown, Xiche Hu, and R. Travis Taylor

Poster 77
Evolution of a bacterial global regulator
Yvette Unoarumhi, Robert Blumenthal and Jyl Matson

Poster 79
Bioinformatics analysis combined microarray identify mutations in nonsense-mediated mRNA decay (NMD) in Breast Cancer
Shahrzad Eslamian

Poster 81
Consequences of simulated biologically realistic processes for population genetic structure
Scott Thomas

Poster 83
An analysis of microbial involvement in biospeleogenesis within lechuguilla cave system
Garrett Sonntag, Hazel Barton and Max Wisshak

Poster 85
Identification of protein-protein interaction sites between HIV-1 reverse transcriptase and integrase using coevolutionary analysis
Madara Hetti-Arachchilage, Kendall Furbee, and Helen Piontkivska

Poster 87
Molecular characterization of surgically induced cervical syringomyelia
Ashley Wilkinson-Mohrman, Mahmoud Farrag, Stephanie Haft, He Huang, Leah Shriver and Nic Leipzig

Poster 89
Finding time-patterns in temporal gene expression data
Guenter Tusch, Raveena Pedyam, Shahrzad Eslamian, Swati Gupta and Christopher Theisen

Poster 91
RNA-Seq to study music perception
Preethy Sasidharan Nair, Anju Philips, Harri Lähdesmäki, and Irma Järvelä

Poster 93
A multi-layers network framework for clustering high-throughput biological data across species
Koon-Kiu Yan, Daifeng Wang, Paul Muir, Joel Rozowsky, and Mark Gerstein

Poster 95
An ant colony pairwise alignment based on the simplified grid
Xinyuan Zhou and Dachao Li

Poster 97
SNPGenie: a software platform for detecting natural selection in pooled next-generation sequencing samples
Chase W. Nelson and Austin L. Hughes

Poster 99
Towards efficient clustering of genomic data
Surbhi Bhatnagar and Jaroslaw Meller

Poster 101
Alternative splicing and mutations of splicing factors and their implications in acute myeloid leukemia
Meenakshi Venkatasubramanian and Nathan Salomonis

Poster 103
Implicating a multi-cellular interactome that integrates cell-specific differentiation, branching morphogenesis, and vascular and organ-scale patterning during the saccular phase of lung development
Yunguan Wang, Anil Jegga, Eric Brunskill, Steven Potter, Jeffery Whitsett, and Bruce Aronow

Poster 105
Bioinformatics multidimensional data viewing and analysis with parallel coordinates
Alexander Addy, Zhong-Hui Duan, and Yingcai Xiao

Poster 107
Structure-based prediction of homeodomain binding site specificity using an integrative energy function
Alvin Farrel and Jun-Tao Guo

Poster 109
PhagePhisher: a method for the location of occult viral sequences in complex genomic datasets
Thomas Hatzopoulos, Catherine Putonti and Siobhan Watkins

Poster 111
SeqOnce: Flexible mobile entrez database search app
Fathi Mubaraki


Poster Sessions B - Wednesday, 10:00am - 11:30am

Poster 2
Development of ProtSecKB: the protist secretome and subcellular proteome knowledgebase
Brian Powell Xiangjia Min Vamshi Amerishetty John Meinken Feng Yu and Chester Cooper

Poster 4
Protein side-chain conformation prediction methods are accurate in different residue environments
Lenna Peterson Xuejiao Kang and Daisuke Kihara

Poster 6
Functional characterization of healthy adult human brain and its application to study neurological disorders
Simarjeet Negi and Babu Guda

Poster 8
PL-PatchSurfer2.0: A fast virtual screening program using surface patch based on 3D Zernike descriptors
Woong-Hee Shin and Daisuke Kihara

Poster 10
Fitting of multiple protein chains by iterative manipulation of Cry-EM maps
Lyman Monroe and Daisuke Kihara

Poster 12
MAGNA++: Maximizing accuracy in global network alignment via both node and edge conservation
Vipin Vijayan Vikram Saraph and Tijana Milenkovic

Poster 14
Understanding how endosymbiosis of a bacterium changes the metabolic potential of the pathologic nematodes Onchocerca volvulus and Loa loa
Nirvana Nursimulu Swapna Lakshmipuram Seshadri and John Parkinson

Poster 16
Modified regularized markov clustering for community detection in attributed networks
Rachael Blair and Han Yu

Poster 18
SEGEL: a database of smoking effects on human lung gene expression
Yin Lu Yan Xu and Feng Cheng

Poster 20
Hypergraphs for complex biological networks
Graham Cromar Alex Yang Anthony Zhao and John Parkinson

Poster 22
Diffhunter: A general scalable framework for comparing genome-wide protein occupancy profiles to study protein-RNA interactomes Seyedsasan Hashemikhabir, Vishal Kumar Sarsani, and Sarath Chandra Janga

Poster 24
Combination of data pre-processing and principal component analysis improves the characterization of biological data
Bin Xue

Poster 26
Detecting fossils of horizontal gene transfer between symbiotic species
Jonathon Brenner and Catherine Putonti

Poster 28
TophatFusion FusionCatcher and Genomon
Morris Chukhman, Mark Maienschein-Cline, Cong Liu, Morris Chukhman, Hui Lu, Zhengdeng Lei, Pinal Kanabar, Oleksiy Karpenko, Georgi Genchev, and Neil Bahroos

Poster 30
Application of healthy human brain gene expression model to study neurological disorders
Simarjeet Negi and Babu Guda

Poster 32
Predicting protein druggability using only sequence composition
Gaurav Kandoi Marcio Luis Acencio and Ney Lemke

Poster 34
Metabolic dysregulation in the cuprizone multiple sclerosis model
Alexandra Taraboletti and Leah Shriver

Poster 36
A comparative analysis of the genetic relationships between the pathogens of Ebola Haemorrhagic Hever, Marburg virus, HIV, Hepatitis A, Hepatitis B, Hepatitis C, Hepatitis D, and Hepatitis E
Olaitan Awe, Segun Fatumo, Olugbenga Oluwagbemi, and Angela Makolo

Poster 38
COMET ("COalescence with multiple mergers employing thermodynamic integration")
Edward Salinas, John Horne, and Rita Castilho

Poster 40
Expression analysis of affinity isolated glial-nuclei from Drosophila larvae
Jingqun Ma and Vikki Weake

Poster 42
Bioinformatic identification and analysis of extensins in the plant kingdom
Xiao Liu, Richard Wolfe, Lonnie Welch, and Allan Showalter

Poster 44
Characterizing the Source-Sink dynamics of Tomato Yellow Leaf Curl Virus (TYLCV) using Bayesian phylogeography methods
Batsirai Mabvakure, Gordon Harkins, and Leendert Cloete

Poster 46
CT-Finder: a web service for designing single and paired guide RNA for CRISPR/Cas9 system
Houxiang Zhu, Lauren Misel, and Chun Liang

Poster 48
Mirpro: a novel program for differential expression and variation analysis of miRNAs
Jieming Shi, Lei Li, Min Dong, Lin Liu, Agustin Madrigal, Katia Del Rio-Tsonis, and Chun Liang

Poster 50
Prediction of piRNAs using transposon interaction and a support vector machine
Kai Wang, Chun Liang, and Fei Li

Poster 52
Workflow configurations for high throughput human variant calling
Liudmila Sergeevna Mainzer, Arjun Prasanna Athreya, Subho Sankar Banerjee, Ravishankar Iyer, Volodymyr Kindratenko, and Victor Jongeneel

Poster 54
Detecting double-stranded RNA viruses in infected host cells
Mark Maienschein-Cline, Pinal Kanabar, Zhengdeng Lei, Morris Chukhman, Neil Bahroos, Stefan Green, and Howard Lipton

Poster 56
A pathway-based genomic classifier for prediction of gastric cancer subtypes

Zhengdeng Lei, Pinal Kanabar, Mark Maienschein- Cline, Oleksiy Karpenko, Morris Chukhman, and Neil Bahroos

Poster 58
A novel alignment-free searching algorithm for fusion gene detection from RNA-Seq short reads
You Li and Chittibabu Guda

Poster 62
Agent-based simulation of stable host-pathogen communities
Roy Williams and Amar Das

Poster 64
Classification of breast cancer tumors based on somatic mutation profiles
Suleyman Vural, Xiaosheng Wang, and Chittibabu Guda

Poster 66
Synergistic regulatory function of driver and passenger strands in MicroRNA-574
Qiuqing Wang and Peng Yao

Poster 68
Comparison of methods for estimating tissue components in mixed-tissue samples
Xuerong Liu, Xiao-Qin Xia, Sujay Datta, and Zhenyu Jia

Poster 70
Comparative analysis of gene expression profiles perturbed by lupus inducing drugs
Frazier Baker and Aleksey Porollo

Poster 72
Improving SNV validation of Ion-based sequence data by using GATK metrics
Rodrigo F Ramalho, Renan Valieris, Claudia Andrade, Bruna Barros, Elisa Napolitano, Jorge de Souza, Sandro de Souza, and Dirce Carraro

Poster 74
Computational tools for avian transcriptomics
Kelly Boyd, Emma Highland, Amanda Misch, Catherine Putonti, and Sushma Reddy

Poster 76
Light alters several wave-associated spiking properties of retinal ganglion cells
Daniel Vicarel and Jordan Renna

Poster 78
Connecting Alzheimer’s disease, Parkinson’s disease, and type 2 diabetes through disease network models and enrichment analyses
Walter Jessen, James Sefton, Jodilyn Phillips, and Bruce Gitter

Poster 80
Effects of bench height variation on muscle activation in pianists
Sarah Welch

Poster 82
An analysis of microbial communities present in brewery water source
Olivia S. Hershey and Hazel A. Barton

Poster 84
Integrative molecular characterization of glioblastoma
Kristin Wipfler and Chittibabu Guda

Poster 86
No longer a neglected tropical disease: Molecular evolution of Ebola informed by the latest epidemic
Mary Halpin and Helen Piontkivska

Poster 88
Global peak alignment for comprehensive two-dimensional Gas Chromatography coupled with Mass Spectrometry (GC×GC-MS)
The-Minh Tran, Hengguang Li, Xiang Zhang, and Seongho Kim

Poster 90
An interface to search time-oriented functional genomics databases
Guenter Tusch, Swati Gupta, Shahrzad Eslamian, Raveena Pedyam, and Christopher Theisen

Poster 92
A dynamic model for glucocorticoid receptor-induced gene expression time courses

Samuel Hokin and M. Kathryn Barton

Poster 94
The structural dynamic effects of inhibitor binding to protein kinase C βII

Shashank Jariwala, Sivaraj Sivaramakrishnan, and Barry Grant

Poster 96
Whole genome methylation analysis of Arabidopsis silencing mutants shows a broad role for mRNA-derived siRNAs in methylation of transposons
Kaushik Panda, Lexiang Ji, Drexel A Neumann, Andrea D McCue, Sarah Choudury, Robert J Schmitz, and R Keith Slotkin

Poster 98
Isogenic modeling of RBM20 disease mutations in iPS cells to define direct splicing targets
Aishwarya Kulkarni and Nathan Salomonis

Poster 100
Development of a text-Based classifier tool to identify immunology-related NIH Grants
Fenglou Mao, Charles Hackett, Daniel Rotrosen, and Dawei Lin

Poster 102
Flexible protein structure alignment method based on the residue-residue interaction
Genki Terashi and Mayuko Takeda-Shitaka

Poster 104
Assessment of gene 3’ untranslated region (3’UTR) expression in Neuroplasticity
Benjamin Harrison, Jeff Petruska, and Eric Rouchka

Poster 106
Functional basis of microorganism classification
Chengsheng Zhu, Tom Delmont, Timothy Vogel, and Yana Bromberg

Poster 108
Gene identification and strain classification using Random Forests
John Santerre, Sebastien Boisvert, Jim Davis, Fangfang Xia, and Rick Stevens

Poster 110
Zebrafish Leptin a morpholino-knockdown vs. rescue microarray comparative gene expression analysis
Matthew Tuttle, Mark Dalman, and Richard Londraville