Great Lakes Bioinformatics Conference 2015

HANDOUTS

Rick Westerman, Bioinformatics specialist at the Genomics Facility, Department of Horticulture and Landscape Architecture, Purdue University (pdf)

Great Lakes Bioinformatics Conference 2015

POSTER PRESENTATIONS

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

• Poster Session A - Tuesday, 5:30pm - 7:00pm
• Poster Sessions B - Wednesday, 10:00am - 11:30am
  (Click here to go directly to Poster Sessions B)

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

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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

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Great Lakes Bioinformatics Conference 2015

GLBIO DETAILED AGENDA

As of May 17, 2015. Schedule and locations are subject to change. Please check back for updates. A printed agenda will be available on site in the conference program book.

All rooms are in the Stewart Center on the Purdue campus unless otherwise noted.

Go directly to: [Monday] [Tuesday] [Wednesday]

Great Lakes Bioinformatics Conference 2015

INVITED SPEAKERS

Updated: May 12, 2015

Each GLBIO scientific session is organized around a particular theme, and opens with a leading researcher as an invited speaker.

• Anna Goldenberg, University of Toronto
  Omic data integration - striving towards personalized medicine
• Chad Myers, University of Minnesota
  Mining chemical-genetic interaction networks for genome-wide discovery of new molecular probes
• Hyonho Chun, Purdue University
  Heterogeneous data integration: heritability estimation from multiple phenotypes
• Jeffrey M. Kidd, University of Michigan
  Paralog-specific copy-number variation detection using exact k-mer matching
• Matthew Hahn, Indiana University
  Phylogenomics and the Procrustean bed of the species tree
• Tijana Milenkovic, University of Notre Dame
  Redefining homology by transferring function between conserved network regions
• Yunlong Liu, Indiana University Purdue University Indianapolis
  Roles of regulatory variants in complex disease
• Yuzhen Ye, Indiana University
  Targeted analysis of metagenomes: what’s working and what’s not
• Yana Bromberg, Rutgers University, Functional basis of microorganism classification
• Russell Schwartz, Carnegie Mellon University, What sequencing can (and can't) tell us about tumor evolution

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Great Lakes Bioinformatics Conference 2015

WORKSHOPS

last edit: April 21, 2015

GLBIO Workshops Announced!

Please join us on May 18 for two timely and informative workshops! Bioinformatics Cores and Exploring and Refining Core Competencies for Bioinformatics

1.  GLBIO 2015 BIOINFORMATICS CORES WORKSHOP
Location: 214A

Summary:  The Bioinformatics Cores workshop will bring together leaders of some regional bioinformatics core facilities to present information on the formation and running of a bioinformatics ”Core Facility” including scientific and business aspects of a core.  The workshop will consist of 2 phases.  The first hour will be 3 short presentations by bioinformatics core leaders, who will speak about different aspects of Bioinformatics Core Facilities.  (1) How to establish a core. (2) Hurdles in building a business. (3) Meeting the needs of changing technology.

Program:  The speakers will address the following questions:

• How do you build a core?
• Business model, staffing, service, funding and support, etc.
• How their core operates?  What skills are needed?
• How they interact with scientists & assist research?
• What are the important components to a successful bioinformatics core?

The second hour will be devoted to a Q & A session with the speakers and the audience.  Some starter questions and surveys are listed below:

• Does your school have a core?
• Do they charge for service?
• How big is the core (people)?
• What kinds of service are provided?
• Cost, turnaround time?
• Do they work for only one group?
• Do they develop software tools? Or just use existing tools?
• For those without Cores, what would they like to see at their school?
• Would there be a use for a regional facility that would help other smaller schools?

2. EXPLORING AND REFINING CORE COMPETENCIES FOR BIOINFORMATICS
Location: 214A

Summary:  Bioinformatics professionals work in a variety of settings, including core facilities, biological and medical research labs and software development organizations. The need for bioinformatics skills permeates academia, industry and thehealthcare sector. As the organization, analysis and interpretation of vast amounts of data become central to biomedical research, how do we define bioinformatics competency requirements for these diverse roles and how do we ensure that there is adequate training to meet their needs? The ISCB curriculum task force has drafted a set of core competencies (see http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003496) for three distinct types of bioinformatics professional - the user, the scientist and the engineer. In this workshop we will explore these competencies, learn how they are being used to shape training programs in different contexts, and work together to provide input into a refined and updated set of core competencies.

Program:

• Why core competencies? An overview of the ISCB curriculum guidelines (20 min)
  
  - Cath Brooksbank, European Molecular Biology Laboratory and European Bioinformatics Institute
  - Lonnie Welch, Ohio University 
• Applying core competencies to teaching bioinformatics engineers (15 min)
  - Predrag Radivojac, Indiana University 
• Applying core competencies to teaching bioinformatics scientists (15 min)
  - Russell Schwartz, Carnegie Mellon University 
• Q&A (10 min)
• Breakout sessions (30 min): We will split into two groups representing the scientist and the engineer; using the competency profiles defined by the ISCB task force, we will consider (1) what level of each competency is required for the role under discussion - general awareness, working knowledge or specialist knowledge? We will also consider the evidence that we would want to gather to convince ourselves that someone had a specific competency.
• Report back from scientist breakout (10 mins)
• Report back from engineer breakout (10 mins)
• Discussion and wrap up (10 mins)

Outcomes:  Participant input will be combined with input from other workshops to generate a consultation paper on bioinformatics competency, with the aim of gathering broad community input on competency requirements in bioinformatics.

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Great Lakes Bioinformatics Conference 2015

TUTORIALS - Monday, May 18

last edit: April 28, 2015

CourseSource - Robin Wright, Department of Biology Teaching and Learning; Department of Plant Biology, University of Minnesota -http://www.coursesource.org/ 

Course Description:  Publishing Teaching Materials in CourseSource, a New Peer-reviewed, Open-access Journal for Undergraduate Biology Education

Improving biology education by publishing in CourseSource, a peer-reviewed, open-access journal of teaching resources - In response to the many national calls for transformation of undergraduate science education, colleges and universities nationwide are beginning to approach their undergraduate science courses in new ways.  Unfortunately, change has been slow and fragmented.  One of the greatest hurdles to undergraduate education transformation is the time, energy, and vision that instructors need to create evidence-based lessons, courses, and curricula.  With support from the Howard Hughes Medical Institute and in collaboration with scientific societies, a new peer-reviewed, open-access journal called CourseSource (coursesource.org) is now available.  CourseSource publishes field-tested activities that implement best practices in scientific teaching and that address learning goals determined by scientific societies. 

This workshop will begin with a review of the CourseSource article format, review criteria, and submission process.  Participants will then be able to consult about their ideas for articles and to begin work on a potential submission.  Each participant should leave with an outline for at least one contribution to this new journal. 

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Medical Imaging - Li Shen, Indiana University - www.iu.edu/~shenlab/

Course Description: Today's generation of multi-modal imaging systems produces massive high dimensional data sets, which when coupled with high throughput genotyping data such as single nucleotide polymorphisms (SNPs), provide exciting opportunities to enhance our understanding of phenotypic characteristics and the genetic architecture of human diseases. However, the unprecedented scale and complexity of these data sets have presented critical bottlenecks requiring new concepts and enabling tools. In this talk, using the quantitative genetics study of the Alzheimer's Disease Neuroimaging Initiative (ADNI) data as an example, we discuss the recent development of bioinformatics strategies for multidimensional brain imaging genomics. We review and synthesize ADNI genetic associations with disease status or quantitative disease endophenotypes including structural and functional neuroimaging, fluid biomarker assays, and cognitive performance. We briefly discuss the diverse analytical strategies used in these studies, and present a very recent study on transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm. We perform pathway and network enrichment analyses of these ADNI genetic associations to highlight key mechanisms that may drive disease onset and trajectory. We show that the broad availability and wide scope of ADNI genetic and phenotypic data has advanced our understanding of the genetic basis of AD and has nominated novel targets for future studies.

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NGS Sequencing - Rich McEachin, University of Michigan - www.ccmb.med.umich.edu/node/244

Course Description: RNA-Seq data analysis tutorial
RNA-Seq is a method of assessing gene expression and differential gene expression using high throughput DNA sequencing technology (Next Generation Sequencing or NGS). Today’s workshop will introduce RNA-Seq technology and RNA-Seq data analysis, and demonstrate an application.  We will start from raw reads data and proceed through the analysis to develop a report that would be appropriate to give to a Core customer. This pipeline uses the familiar Tuxedo Suite as the engine driving alignment, quantitation of expression, and differential expression analysis. Beyond these basics, the pipeline performs extensive quality control and error checking, reporting, and formatting of output to make it user friendly. In addition, the RNA-Seq pipeline is a tool for testing competing approaches to RNA-Seq data analysis, allowing us to assess the effectiveness of new algorithms or software in parallel with our primary analyses. Note that the raw reads data used in this analysis are publicly available and we provide a script that would allow a user to perform a simplified analysis at a later date. While “just the basics”, this simplified analysis would allow a user to get a feel for the essentials of the task, as well as to explore parameter settings and gain a deeper understanding of the process.    
          
Biography:  Rich is a research faculty member in the Department of Computational Medicine and Bioinformatics (DCMB) at the University of Michigan, working primarily in the Bioinformatics Core (one of the UM Biomedical Research Core Facilities). Rich’s education emphasizes statistics and genetics, and he has more than ten years of experience in the field. Rich has been extensively involved in developing, testing, refining, and using the analysis pipeline the Core uses for RNA-Seq data analysis. The UM Bioinformatics Core performs a wide range of bioinformatics analyses (e.g. RNA-Seq, ChIP-Seq, Exome-Seq, assembly, systems biology, custom analyses) providing services to investigators who have sophisticated analysis needs but who do not have the necessary analytical skills, software, or hardware in-house. The UM Bioinformatics Core serves the needs of researchers at the University of Michigan and across the Great Lakes region.

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Personalized Medicine - Yana Bromberg, Rutgers University -
bromberglab.org/?q=people

Course Description:  The goal of this workshop is to provide a broad overview the history, advances and current state of the art in customization of medical care, i.e. personalized medicine. It will be formatted in an outline of a conceptual personalized medicine pipeline, which, we hope, one may see in a doctor's office one day. We will describe the ideas and approaches, tools and data sources, required to analyze and draw inferences relevant to specific individual genetics. We will highlight problems with existing techniques and findings (e.g. exactly how significant are findings of GWAS annotated diseases SNPs in an individual’s genome?) and propose potential solutions using available data (e.g. computational means of narrowing down whole-genome variation to that which might be disease-causing). Finally, we will discuss some examples of existing and, arguably, most actionable applications of personalized medicine – pharmacogenomics findings. We will also peek into the possible future of this science (e.g. how should the "personal metagenome" be incorporated into personalized medicine) and discuss some of the ethical questions and implications of application of personalized medicine. The workshop will be in a seminar format, i.e. lecture with lots of space for discussion.

Biography:  Dr. Bromberg is an assistant professor at the Department of Biochemistry and Microbiology, Rutgers University. She also holds an adjunct assistant professor position at the Department of Genetics at Rutgers and has recently become a fellow at the Institute of Advanced Studies in the Technical University of Munich. She received her Bachelor's degrees in Biology and Computer Sciences from the State University of New York at Stony Brook and a Ph.D. in Biomedical Informatics from Columbia University, New York. Dr. Bromberg is known for her seminal work on a method for screening for non-acceptable polymorphisms, or SNAP for short, which evaluates the effects of single amino acid substitutions on protein function. Currently, her research is focused on the analysis of human variomes for disease predisposition, functional annotation of microbiomes, and the study of evolution of life's electron transfer reactions. Her work was recognized by several awards, including the Hans-Fischer award for outstanding early career scientists and recognition for the top performance in the Critical Assessment of Genome Interpretation experiment. Dr. Bromberg actively participates in organizing the ISMB/ECCB conferences (ISMB stands for Intelligent Systems for Molecular Biology, and ECCB is its European equivalent). She chairs this year's overall Disease theme of the conference, as well as poster-and-talk sessions. She conducts workshops, and organizes a special interest group aimed at the study of genomic variation -- VarI-SIG. Dr. Bromberg also serves as an editor and a reviewer of several top bioinformatics journals. For more information see http://bromberglab.org/

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Great Lakes Bioinformatics Conference

PROGRAM Book

Click here to download (pdf)

STAY CONNECTED

@GLBIO15

THANK YOU FOR MAKING GLBIO 2015 AT PURDUE A HUGE SUCCESS!  With over 250 attendees, outstanding education, the celebration of GLBIO's tenth anniversary and 118 poster presentations, GLBIO 2015 was a rousing success!

GLBIO is pleased to recognize the following award winners

Full paper:  James Pease and Benjamin Rosenzweig - The multisample variant format (MVF) for phylogenomics and population genomics

Ten minute talk:  Deborah Chasman, Kevin Walters, Amie Eisfeld, Yoshihiro Kawaoka and Sushmita Roy - Integrative reconstruction of the regulatory network controlling host response to influenza infections 

Posters – three winners (in order of poster number):

#93 – Daifeng Wang - A multi-layers network framework for clustering high-throughput biological data across species

#97 – Chase Nelson - SNPGenie: a software platform for detecting natural selection in pooled next-generation sequencing samples

#108 – John Santerre - Gene identification and strain classification using Random Forests 

Don't forget to check out our job postings - Click here for job description (pdf)  Bioinformatician I – Purdue - Cyber Center  
Look for more information in the Fall about GLBIO 2016 in Toronto - May 16-19, 2016. For any GLBIO questions, please contact Ms. Cori Dossett, meeting planner, at This email address is being protected from spambots. You need JavaScript enabled to view it..

STUDENT ACTIVITIES PHOTO ALBUM

Great Lakes Bioinformatics Conference 2015

 STEERING COMMITTEE

Updated October 8, 2014

• Lonnie Welch, Ohio University (Steering Committee Chair)
• Bruce Aronow, Childrens Hospital Medical Center, University of Cincinnati (Ex-Officio)
• Sorin Draghici, Wayne State University  (Ex-Officio)
• Jundong Liu, Ohio University
  
• Russell Schwartz, Carnegie Mellon University (Ex-Officio)